data collection and refinement statistics (37)

elife-26738-v1.xml

10.7554/eLife.26738.006

Table 1.Data collection and refinement statistics.

Values in parentheses are for the highest-resolution shell.

	preS1-2H5 scFv
Data collection
Space group	P2₁2₁2
Cell dimensions
a, b, c (Å)	142.7, 55.7, 67.7
α, β, γ (°)	90, 90, 90
Wavelength (Å)	0.9793
Resolution range (Å)	20–2.5 (2.54–2.50)
Unique reflections	18558(886)
Redundancy	5.8 (5.9)
<I > /<σ(I)>	17.7 (6.2)
Completeness (%)	96.0 (94.9)
R_merge	0.144 (0.345)
Refinement
Resolution range (Å)	20–2.5 (2.90–2.50)
No. reflections	18265
No. atoms	3747
Protein	3519
Water	227
Ion	1
R_work	0.231 (0.292)
R_free	0.283 (0.356)
Mean B factor (Å²)	14.5
Rmsd bond length (Å)	0.002
Rmsd bond angles (°)	0.555

elife-29236-v1.xml

10.7554/eLife.29236.005

Table 1.Data collection and refinement statistics

Data collection
Space group	P6₄22
Cell dimensions a, b, c (Å) α, β, γ (°)	123.8, 123.8, 174.0 90, 90, 120
Beamline	Diamond i03
Wavelength (Å)	2.0
Resolution (Å)	107.83–2.19 (2.25–2.19)
Number of observed reflections	1877448
Number of unique reflections	41684
Completeness (%)	99.9 (99.9)
R_merge (%) *	9.8 (223.4)
I/δ	32.3 (1.6)
Multiplicity	45.0 (18.2)
Anomalous completeness (%)	99.9 (99.8)
Anomalous multiplicity	23.7 (9.4)
Anomalous slope	1.169
Refinement statistics
R_work (%) †	20.1
R_free (%) ‡	21.6
Ramachandran favored (%)	97.24
Ramachandran allowed (%)	99.08
MolProbity score/percentile §	1.61/97
Averaged B-factor (Å²)	63.47
Rmsd bond length (Å)	0.905
Rmsd bond angles (°)	1.007

The values in parenthesis refer to the highest resolution shell.

^*Rmerge=∑hkl∑i|I(hkl;i)−<I(hkl)>|∑hkl∑i(hkl;i) where I(hkl;i) is the intensity of an individual measurement of a reflection and <I(hkl)> is the average intensity of that reflection.

^†Rwork=∑hklF0−Fc∑hklF0 where F0andFc are the observed and calculated structure factors, respectively.

‡ R_free is R_work with 5% of the observed reflections removed before refinement.

§ MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution. 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006 (Chen et al., 2010).

elife-29428-v2.xml

10.7554/eLife.29428.012

Table 1.Data collection and refinement statistics

AMPylated haBiP^28-549	Apo	Apo	Apo	ADP	ADP
Data collection
Synchrotron stations (DLS)	I02	I24	I24	I24	I24
Space group	P2₁	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁
Cell dimensions
a,b,c; (Å)	68.33, 118.65, 83.15	64.65, 69.07, 122.23	69.088, 75.408, 98.308	69.089, 75.310, 98.350	69.05, 75.61, 97.50
α, β, γ; (⁰)	90, 97, 90	90, 90, 90	90, 90, 90	90, 90, 90	90, 90, 90
Resolution, (Å)	67.76–1.86 (1.91–1.86)*	61.12–2.0 (2.05–2.00)	75.41–1.67 (1.7–1.67)	98.35–1.71 (1.74–1.71)	97.5–1.59 (1.61–1.59)
R_merge	0.089 (0.83)	0.158 (1.31)	0.086 (0.794)	0.096 (1.002)	0.131 (0.906)
R_meas	0.122 (1.119)	0.185 (1.532)	0.096 (0.871)	0.108 (1.104)	0.145 (1.022)
<I/σ (I)>	9.6 (1.4)	8.5 (1.5)	12 (2.1)	13 (2.2)	8.8 (2.2)
CC_1/2	0.995 (0.533)	0.995 (0.522)	0.997 (0.888)	0.998 (0.820)	0.990 (0.836)
Completeness, %	99.4 (99.1)	99.9 (100)	98.3 (100)	99.9 (100)	100 (99.9)
Redundancy	3.4 (3.5)	7.1 (7.2)	6.6 (6.7)	6.6 (6.7)	6.5 (6.4)
Refinement
R_work	0.195	0.240	0.210	0.210	0.200
R_free	0.212	0.280	0.250	0.250	0.220
No. of reflections	104104	35827	56476	53637	66447
No. of atoms	8750	3994	4281	4245	4156
Average B-factors	24.9	35.7	23.14	23.3	30.09
RMS deviations
Bond lengths (Å)	0.007	0.007	0.007	0.009	0.008
Bond angles, (⁰)	1.261	1.151	1.184	1.485	1.332
Ramachandran favoured region, %	99	97.49	98.05	98.44	99.03
Ramachandran outliers, %	0.19	0	0	0	0
MolProbity score (percentile^†)	0.67 (100%)	0.83 (100%)	0.67 (100%)	0.78 (100%)	0.74 (100%)
PDB code	5O4P	6EOB	6EOC	6EOE	6EOF

* Values in parentheses are for the highest-resolution shell.

^†100th percentile is the best among structures of comparable resolution.

elife-31529-v1.xml

10.7554/eLife.31529.016

Table 1.Data collection and refinement statistics.

Figures in parentheses are for the highest resolution shell.

Wavelength	0.9724
Resolution range (Å)	44.7–2.45 (2.51–2.45)
Space group	P1
Unit cell (Å, °)	a = 74.0, b = 90.5, c = 90.9, α = 110.78, β = 98.99, γ = 114.11
Total no. reflections	246972 (15753)
No. unique reflections	67728 (4517)
Multiplicity	3.6 (3.5)
Completeness (%)	97.8 (97.3)
Mean I/σ(I)	7.4 (1.0)
Wilson B-factor (Å²)	63.3
R_merge (I)	0.093 (1.058)
R_meas (I)	0.109 (1.243)
R_pim (I)	0.055 (0.639)
CC(½) (I)	0.997 (0.495)
Reflections used in refinement	67723
Reflections used for R_free	3353 (5%)
R_model (F)	0.205 (0.221)
R_free (F)	0.238 (0.265)
Number of non-hydrogen atoms:
macromolecules	12919
ligands	284
water molecules	129
rms deviation from ideal geometry (bonds)	0.010
rms deviation (angles)	1.11
Ramachandran favored (%)	97.7
Ramachandran allowed (%)	2.1
Ramachandran outliers (%)	0.2
Rotamer outliers (%)	3.5
Clashscore	3.22 (100th percentile)
Wilson B-factor (Å²)	63.3
Average B-factors (Å²):
macromolecules	66.5
ligands	69.5
solvent	54.0

elife-32893-v1.xml

10.7554/eLife.32893.005

Table 1.Data collection and refinement statistics

	Y608 peptide complex	Y628 peptide complex	Y658 peptide complex
Crystal parameters
Space group	P6₄	P6₄	P6₄
Cell dimensions:
a, b, c (Å)	126.07, 126.07, 73.40	126.19, 126.19, 74.11	125.48, 125.48, 74.14
α, β, γ (°)	90, 90, 120	90, 90, 120	90, 90, 120
Data collection
Wavelength (Å)	1.000	1.000	1.000
Resolution (Å)	50–2.63 (2.68–2.63)*	50–3.10 (3.15–3.10)	50–2.60 (2.64–2.60)
No. of unique reflections	20035	12419	20659
Multiplicity	11.3 (10.9)	11.3 (11.4)	11.4 (11.5)
Completeness (%)	100 (100)	100 (100)	100 (100)
R_meas	0.078 (1.504)	0.103 (1.880)	0.094 (2.069)
R_pim	0.023 (0.455)	0.031 (0.556)	0.028 (0.608)
CC_1/2	(0.743)	(0.646)	(0.780)
Mean I/σ	28.1 (1.8)	24.8 (1.6)	26.5 (1.6)
Refinement
Resolution (Å)	43–2.62	36–3.10	36–2.60
No. of reflections	19977	12322	20589
R_work/R_free	0.185/0.223	0.194/0.251	0.192/0.227
RMSD bond lengths (Å)	0.008	0.010	0.009
RMSD bond angles (°)	0.948	1.194	0.965
No. of atoms
Protein/peptide	2003	2121	2118
Water/ion	2	0	34
Ramachandran plot
Favored (%)	95.5	92.3	95.4
Outliers (%)	0	0	0
PDB accession code:	5WRK	5WRL	5WRM

*Values in parentheses are for highest resolution shell.

elife-32963-v1.xml

10.7554/eLife.32963.015

Table 1.Data collection and refinement statistics

	HOXB13-DNA^TCG	HOXB13-DNA^CAA	CDX2-DNA^TCG	CDX2-DNA^CAA
Data collection
Wavelength (Å)	0.9724	0.9724	0.9724	0.9724
Resolution range (Å)	46.29–3.2 (3.31–3.2)	45.95–2.19 (2.27–2.19)	43.23–2.57 (2.66–2.57)	55.96–2.95 (3.13–2.95)
Space group	P 2 2 2₁	P 1 2 1	C 1 2 1	I 1 2 1
Unit cell (Å, °)	52.62 52.52 389.33; 90 90 90	77.35 57.92 101.28; 90 101.57 90	127.95 46.49 68.89; 90 113.27 90	70.25 46.69 128.63; 90 101.40 90
Total reflections	86877 (3476)	241614 (21747)	19575 (1958)	27018 (4003)
Unique reflections	17526 (1361)	44125 (3912)	12095 (1197)	8802 (1264)
Multiplicity	4.2 (3.3)	5.5 (5.6)	1.6 (1.6)	3.2 (3.2)
Completeness (%)	93.0 (90.4)	97.42 (87.37)	99.5 (100)	96.6 (90.5)
Mean I/sigma(I)	7.91 (0.10)	8.11 (1.10)	8.47 (2.77)	7.5 (1.1)
R-merge	0.085 (4.59)	0.12 (1.21)	0.13 (5.49)	0.071 (7.24)
R-meas	0.09	0.13	0.08	0.09
CC1/2	0.99 (0.72)	0.99 (0.71)	0.99 (0.80)	0.99 (0.61)
Refinement
R-work	0.21	0.25 (0.37)	0.22	0.19
R-free	0.28	0.29 (0.35)	0.29	0.25
Number of non-hydrogen atoms	5197	5591	2841	2783
macromolecule	5172	5072	2748	2717
water	8	519	93	66
Protein residues	242	274	144	141
RMS (bonds)	0.025	0.011	0.018	0.012
RMS (angles)	2.03	1.26	2.11	1.83
Ramachandran favored (%)	93	97	97.8	99.3
Ramachandran outliers (%)	1.7	0.41	1.43	0.73
Clashscore	10.51	5.31	4.42	6.43
Average B-factor	124.40	41.70	30.54	74.75
macromolecule	124.70	42.10	29.30	74.41

Statistics for the highest-resolution shell are shown in parentheses.

elife-33111-v2.xml

10.7554/eLife.33111.008

Table 1.Data collection and refinement statistics.

	CPSF160-WDR33
Dataset	Native	Sulfur SAD	Ta₆Br₁₂ SAD
X-ray source	SLS X06DA (PXIII)	SLS X06DA (PXIII)	SLS X06DA (PXIII)
Space group	P₁	P₁	P₁
Cell dimensions
a, b, c (Å)	67.91 77.40 104.02	67.88 77.58 104.14	67.52 76.79 104.02
α, β, γ (^o)	87.56 76.41 67.00	87.39 76.60 66.76	87.36 76.72 66.30
Wavelength (Å)	1.0000	2.0733	1.2548
Resolution (Å)*	47.27–2.50 (2.59–2.50)	44.25–3.00 (3.11–3.00)	47.26–3.60 (3.73–3.60)
R_merge*	0.090 (0.773)	0.211 (2.934)	0.140 (0.669)
CC1/2*	0.999 (0.834)	0.999 (0.847)	0.998 (0.926)
I/σI*	18.3 (2.5)	29.3 (2.5)	20.6 (4.6)
Observations*	488656 (34882)	2456831 (165849)	300048 (29753)
Unique reflections*	65410 (6519)	37770 (3688)	21497 (2126)
Multiplicity*	7.5 (5.4)	65.0 (45.0)	14.0 (14.0)
Completeness (%)*	100.0 (100.0)	100.0 (96.9)	99.9 (99.6)
Refinement
Resolution (Å)	47.27–2.50
No. reflections	65395 (6517)
R_work/R_free	0.228/0.263
No. atoms
Protein	12162
Water	102
B-factors
mean	69.35
Protein	69.52
Water	49.03
R.m.s. deviations
Bond lengths (Å)	0.002
Bond angles (^o)	0.56
Ramachandran plot
% favored	94.6
% allowed	5.4
% outliers	0.0

elife-34317-v1.xml

10.7554/eLife.34317.017

Table 4.Data collection and refinement statistics

	Sb_MBP#1 (PDB: 5M13)	Sb_MBP#2 (PDB: 5M14)	Sb_MBP#3 (PDB: 5M15)
Data Collection
Space group	P2₁2₁2₁ (19)	P2₁2₁2₁ (19)	P2₁2₁2₁ (19)
Cell dimensions
a, b, c (Å)	58.298 82.789 102.583	57.890 57.950 281.540	57.030 57.780 286.530
α, β, γ (°)	90.00 90.00 90.00	90.00 90.00 90.00	90.00 90.00 90.00
Resolution (Å)	50–1.37	50–1.6	50–1.9
R_meas (%) ¹⁾	6.5 (60.9)	5.9 (124)	7.8 (146.6)
I/σ_I	15.26 (3.47)	16.98 (1.82)	21.44 (2.17)
CC_1/2 (%)	99.9 (86.3)	99.9 (68.5)	100 (60.5)
Completeness (%)	99.4 (97.7)	100 (100)	100 (100)
Redundancy	6.1	6.5	12.9
Refinement
Resolution (Å)	50–1.37	50–1.6	50–1.9
No. reflections (work/test)	102618/5131	126118/6307	75931/3797
R_work/R_free (%)	16.82/18.60	19.04/21.56	20.92/25.70
No. atoms
Protein	3873	7640	7619
Water	694	1040	422
B-factor (Å²)
Total	20.1	34.4	50.1
R.m.s deviations
Bond lengths (Å)	0.005	0.003	0.003
Bond angles (°)	0.750	0.591	0.623

1) Values in parentheses are for the last resolution shell

elife-34960-v2.xml

10.7554/eLife.34960.009

Table 1.Data collection and refinement statistics.

Data collection
Space group	P2₁2₁2
Cell dimensions
a, b, c (Å)	92.2, 250.6, 33.8
α, β, γ (°)	90, 90, 90
Wavelength (Å)	1.000
Resolution (Å)*	125–2.65 (2.72–2.65)
R_sym*	7.3 (81.3)
I/σI*	14.9 (2.2)
Completeness (%)*	99.8 (98.4)
Redundancy*	5.4 (5.5)
Refinement
Resolution (Å)	125–2.65
No. of reflections	23830
R_work/R_free (%)	20.8/23.8
No. of atoms
Protein	4851
Ligand/ion	4
Water	64
B-factors (Å²)
Protein	87.6
Ligand/ion	69.3
Water	58.3
R.m.s deviations
Bond lengths (Å)	0.010
Bond angles (°)	0.82

*Highest resolution shell is shown in parenthesis.

elife-34995-v2.xml

10.7554/eLife.34995.016

Table 1.Data collection and refinement statistics.

Statistics for the highest-resolution shell are shown in parentheses.

	PepT_Sh (PDB: 6EXS)
Wavelength	0.8729
Resolution range	45.1–2.5 (2.589–2.5)
Space group	P 1 21 1
Unit cell	60.04 55.576 100.866 90 104.749 90
Total reflections	151797 (14474)
Unique reflections	22501 (2204)
Multiplicity	6.7 (6.6)
Completeness (%)	99.43 (99.73)
Mean I/sigma (I)	9.76 (1.48)
Wilson B-factor	43.87
R-merge	0.159 (1.28)
R-meas	0.172 (1.39)
R-pim	0.07 (0.54)
CC1/2	0.997 (0.59)
CC*	0.999 (0.86)
Reflections used in refinement	22504 (2204)
Reflections used for R-free	1137 (110)
R-work	0.21 (0.21)
R-free	0.23 (0.24)
CC (work)	0.88 (0.69)
CC (free)	0.85 (0.52)
Number of non-hydrogen atoms	4063
macromolecules	3614
ligands	384
solvent	65
Protein residues	487
RMS(bonds)	0.01
RMS(angles)	1.04
Ramachandran favored (%)	98.35
Ramachandran allowed (%)	1.65
Ramachandran outliers (%)	0
Rotamer outliers (%)	1.47
Clashscore	2.59
Average B-factor	57.0
macromolecules	54.72
ligands	80.53
solvent	51.2

elife-35335-v2.xml

10.7554/eLife.35335.004

Table 1.Data collection and refinement statistics

	6ERM	6ERN	6ES8
Data collection
Space group	P6	P6	P6
Cell dimensions
a, b, c (Å)	91.04, 91.04, 56.53	90.85, 90.85, 56.75	91.30, 91.30, 57.20
a, b, g (°)	90.0, 90.0, 120.0	90.0, 90.0, 120.0	90.0, 90.0, 120.0
Resolution (Å)	78.85–2.00 (2.03–2.00)	78.68–2.36 (2.44–2.36)	79.08–1.90 (2.0–1.9)
R_meas	13.3 (59.0)	7.0 (28.7)	8.4 (87.8)
CC_1/2 (%)	99.0 (90.9)	99.8 (95.0)	99.1 (94.3)
I / σI	10.8 (6.1)	15.4 (3.9)	10.8 (1.6)
Completeness (%)	100.0 (100.0)	92.6 (92.6)	91.5 (94.1)
Redundancy	9.3 (9.2)	4.9 (4.7)	4.6 (4.4)

Resolution (Å)	2.0	2.36	1.90
No. reflections	18217	11142	21569
R_work/R_free	0.23/0.18	0.24/0.19	0.22/0.18
No. of atoms	1808	1674	1816
Protein	1569	1562	1623
Ligand/ion	30	30	71
Water	209	82	122
B-factors
Protein	29.0	36.87	33.2
Ligand/ion	71.6	77.49	60.2
Water	36.3	38.39	42.7
R.m.s. deviations
Bond lengths (Å)	0.02	0.017	0.02
Bond angles (°)	1.90	1.82	1.90

*Values in parentheses are for highest-resolution shell.

elife-35946-v2.xml

10.7554/eLife.35946.006

Table 1.Data collection and refinement statistics

Data collection
Microscope	FEI titan krios	FEI titan krios	FEI titan krios
Detector	Falcon III + VPP	K2 Summit + VPP	K2 Summit
Pixel size (Å)	1.07	1.14	0.66
Voltage (kV)	300	300	300
Total electron dose (e^-/Å²)	30	40/40/30	50
Micrographs collected	827	906	2800
Number of frames	75	40/23/30	40
Exposure time (s)	60	10/4.6/6.5	10
Electron dose per frame (e^-/Å²)	0.4	1/1.7/1	1.25
Dose rate (e^-/pixel/s)	0.5	5.2/9/6	2
Frame exposure (s)	0.8	0.25/0.115/0.216	0.25
Total number of particles (after 2D classification)	232,739	313,879	166,313
cryo-EM 3D Refinement
Resolution (Å)	4.11	4.88	6.71
Map sharpening B-factor (Å²)	−130	−150	−529
Fourier shell correlation criterion	0.143	0.143	0.143
Particles used in final 3D refinement	128,002	145,169	72,487
Defocus (μm)	−0.2 to −1	−0.3 to −1.2	−1.2 to −3.5
Coordinate Refinement and Validation
R.m.s. deviations
Bonds (Å)	0.07
Angles (°)	0.984
Ramachandran Favoured (%)	94.6
Ramachandran Allowed (%)	4.89
Ramachandran Outliers (%)	0.51
Molprobity score	1.36
Clashcore, all atoms	0.79
Favoured rotamers	91.12
EMRinger score	1.93
FSC (model vs map - 0.5 cut-off) (Å)	4.08
PDB and map deposition
PDB ID	6GDG
EMDB ID	4390

elife-36154-v2.xml

10.7554/eLife.36154.003

Table 1.Data collection and refinement statistics.

	UbcH7 ~ Ub SidC SNL (PDB ID: 6CP2)	UbcH5C-SdcA SNL (PDB ID: 6CP0)
Data collection
Space group	P6₅22	C222₁
Cell dimensions
a, b, c (Å)	101.522, 101.522, 352.302	135.550, 142.202, 118.333
a, b, g (°)	90.0, 90.0, 120.0	90.0, 90.0, 90.0
Resolution (Å)*	50.0–2.90 (2.95–2.90)	50.00–2.90 (2.95–2.90)
R_sym^† (%)	14.0 (80.2)	12.5 (95.3)
I/σ(I)	30.3 (16.6)	8.8 (2.7)
Completeness (%)	99.9 (99.9)	96.4 (91.5)
Redundancy	13.8 (14.6)	4.0 (3.7)
Refinement
Resolution (Å)	2.9	3.0
No. reflections	27,387	23,102
R_work/R_free^‡ (%)	21.7/28.3	20.3/27.1
R.m.s. deviations
Bond lengths (Å)	0.0113	0.0106
Bond angles (°)	1.4734	1.4619
Ramachandran Plot
Preferred (%)	96.84	96.94
Allowed (%)	3.16	3.06
Disallowed (%)	0	0

*Values in parentheses are for highest-resolution shell.

^†R_sym = Σ_hΣ_i|I_I(h) −<I(h)|/Σ_hΣ_iI_I(h).

elife-36349-v2.xml

10.7554/eLife.36349.012

Table 1.Data collection and refinement statistics

Data collection
Wavelength (Å)	0.9184
Space group	P1
Unit cell parameters
a, b, c (Å)	36.309/43.187/61.859
α, β, γ (°)	80.449/75.485/75.392
Resolution (Å)^a	41.55–2.1 (2.2–2.1)
Unique/observed reflections^a,b	19,931/107,345 (2,633/14,210)
R_sym (%) ^a,c	6.3 (42.9)
I/σI^a	13.96 (3.47)
Completeness (%)^a	97.3 (97.9)
Molecules per asymmetric unit	2
Refinement statistics
R_work (%)^d	18.62
R_free (%)^e	23.34
Number of atoms
Protein	4283
Nucleic acid	574
Water	116
B-factors
Protein	56.062
Nucleic acid	87.427
water	48.058
r.m.s. deviations
Bond lengths (Å)	0.013
Bond angles (°)	1.149

^aHighest-Resolution shell values are given in parentheses.

^bFriedel mates were not treated as independent reflections.

^cR_sym = Σ_h Σ_I | I_i(h) - <I(h)> | / Σ_hΣ_iI(h); where I are the independent observations of reflection h.

^dR_work = Σ_h ||F_obs| - |F_calc|| / Σ_h |F_obs|.

^eThe free R-factor was calculated from 5 % of the data, which were removed at random before the structure was refined.

elife-38017-v2.xml

10.7554/eLife.38017.010

Table 1.Data collection and refinement statistics.

		XaxA	XaxB
Data collection
Wavelength (Å)	SLS PETRA	2.07505 1.8233	0.97793
Resolution range (Å)		44.48–2.5 (2.589–2.5)	48.15–3.4 (3.521–3.4)
Space group		P 21 21 21	P 21 21 21
Cell dimensions a, b, c (Å)		67.27 90.83 153.03	88.7 99.41 194.15
α, β, γ (°)		90 90 90	90 90 90
Molecule no. in AU		2	4
Total reflections		996,585 (92,922)	961,813 (91,076)
Unique reflections		33,174 (3,258)	24,297 (2,378)
Multiplicity		30.0 (28.5)	39.6 (38.3)
Completeness (%)		99.91 (99.94)	99.91 (99.96)
Mean I/σ(I)		25.11 (2.38)	14.23 (0.82)
Wilson B-factor		58.45	137.29
R-merge		0.1055 (1.722)	0.2846 (6.285)
R-meas		0.1073 (1.753)	0.2883 (6.369)
CC1/2		1 (0.872)	0.999 (0.493)
CC*		1 (0.965)	1 (0.813)
Refinement
Reflections used in refinement		33,167 (3,257)	24,289 (2377)
Reflections used for R-free		1659 (173)	1215 (119)
R_work/R_free (%)		23.84/28.57 (35.19/42.56)	26.38/30.52 (37.37/40.11)
CC(work)/CC(free)		0.958/0.943 (0.786/0.715)	0.957/0.941 (0.613/0.442)
Average B-factor (Å²)		77.47	142.42
No. atoms in AU		5373	10,624
Macromolecules		5348	10,624
Solvent		249
Protein residues		678	1329
r.m.s. deviations:
RMS (bonds)		0.004	0.004
RMS (angles)		0.87	0.72
Ramachandran favored (%)		99.4	97.50
Ramachandran allowed (%)		0.6	2.20
Ramachandran outliers (%)		0.00	0.3
Rotamer outliers (%)		1.32	3.82
Clashscore		3.69	3.99

Values for the highest resolution shell are inside brackets.

*For XaxA multiple datasets were collected from one crystal at the PXIII-X06DA beamline at the Swiss Light Source and at the DESY PETRA III beamline P11.

elife-38089-v2.xml

10.7554/eLife.38089.004

Table 1.Data collection and refinement statistics.

	JAK2/EPOR	JAK2/LEPR
Data collection	ALS 5.0.1	SSRL 12–2
Space group	C2	P6₅22
Cell dimensions
a, b, c (Å)	178.49, 114.88, 179.82	263.87, 263.87, 101.08
α, β, γ (°)	90, 93.2, 90	90, 90, 120
Resolution (Å)	48.44–2.65 (2.74–2.65)	43.19–2.83 (2.93–2.83)
R_sym or R_merge	0.073 (0.865)	0.105 (1.60)
I / σI	13.1 (1.3)	21.8 (2.0)
Completeness (%)	99.5 (97.9)	99.6 (99.5)
Redundancy	3.4 (3.3)	13.4 (13.7)
CC1/2	0.99 (0.63)	0.99 (0.80)
Refinement
Resolution (Å)	48.44–2.65 (2.75–2.65)	43.19–2.83 (2.93–2.83)
No. reflections	104,921 (10,233)	49,498 (4853)
R_work/R_free	0.222/0.260	0.228/0.241
No. atoms	16599	7601
Protein	16454	7569
Ligand/ion	N/A	5
Water	145	27
B-factors	71.32	106.19
Protein	71.48	106.30
Ligand/ion	N/A	104.80
Water	53.65	74.23
R.M.S. deviations
Bond lengths (Å)	0.003	0.004
Bond angles (°)	0.85	0.63

Values in parentheses are for highest-resolution shell.

elife-38356-v2.xml

10.7554/eLife.38356.005

Table 1.Data collection and refinement statistics.

	Scc3T/Scc1K native	Scc3T/Scc1K SeMet
Data collection
Space group	P2₁2₁2	P2₁2₁2
Cell dimensions
a, b, c (Å)	109.9, 115.4, 295.6	109.9, 115.6, 296.2
Wavelength (Å)	1.282	1.282
Resolution (Å)	50–3.60	49.9–4.79
No. reflections	20963	10279
R_merge	5.8 (122.6)*	4.6 (112.3)*
I / σI	11.9 (1.6)*	10.6 2(.1)
CC 1/2	0.99 (0.56)	0.99 (0.52)
Completeness (%)	91.4 (63.5)*	93.6 (71.2)*
Redundancy	4.4 (6.0)*	1.8 (1.8)
Refinement
Resolution (Å)	50–3.60
R_work/R_free	0.28/0.31
No. atoms	16465
Protein	14909
DNA	1556
B-factors (mean)
Protein	254.5
DNA	266.4
R.m.s deviations
Bond lengths (Å)	0.002
Bond angles (°)	0.5

*Values in parentheses are for highest-resolution shell.

elife-38958-v2.xml

10.7554/eLife.38958.012

Table 2.Data collection and refinement statistics.

Values in parentheses are for the highest resolution shell.

	Crystal 1	Crystal 2
PDB code		6GPG
Data collection
Space group	P2₁2₁2₁	P6₅22
Wavelength (Å)	1.00	1.00
Cell dimensions
a, b, c (Å)	112.1, 177.1, 314.8	175.6, 175.6, 109.5
α, β, γ (°)	90, 90, 90	90, 90, 120
Resolution range (Å)	47.2–3.3 (3.42–3.30)	46.4–2.9 (3.00–2.89)
R_merge (%)	14.3 (112)	7.6 (206)
I/σI	8.45 (1.28)	19.72 (1.15)
CC_1/2	99.8 (67.6)	99.9 (99.7)
Completeness (%)	95.3 (79.7)	99.7 (97.4)
Redundancy	3.38 (2.91)	13.09 (13.21)
Refinement
Resolution (Å)	3.3	2.9
No. reflections	90,121	22,649
R_work/ R_free	22.8/28.3	21.4/25.9
No. atoms
Macromolecules	35,730	5,810
Ions	10	2
Ramachandran statistics
Favoured (%)	92.78	92.71
Allowed (%)	6.39	6.98
Outliers (%)	0.83	0.31
R.M.S deviations
Bond lengths (Å)	0.011	0.009
Angles (°)	1.48	1.43
B-factors
Macromolecules	109.98	139.89
Ions	105.23	121.74

elife-40444-v2.xml

10.7554/eLife.40444.009

Table 1.Data collection and refinement statistics

	N	n + 1	n + 1, dATP soak	n + 1, dAMPNPP soak	n + 2
Data Collection
Space group	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁	P2₁2₁2₁
Cell Dimensions
a, b, c (Å)	86.1, 93.4, 105.6	88.1, 93.7, 105.8	87.1, 93.5, 105.3	87.44, 93.39, 104.95	87.0, 93.0, 104.7
α, β, γ (°)	90.0, 90.0, 90.0	90.0, 90.0, 90.0	90.0, 90.0, 90.0	90.0, 90.0, 90.0	90.0, 90.0, 90.0
Resolution (Å)	54.31–1.58 (1.64–1.58)	46.09–1.98 (2.05–1.98)	46.7–1.99 (2.06–1.99)	43.72–1.74 (1.78–1.74)	41.04–1.99 (2.06–1.99)
R_merge	0.7309 (1.35)	0.7085 (1.389)	0.1329 (0.7194)	0.0567 (0.241)	0.3279 (1.745)
CC1/2	0.842 (0.795)	0.759 (0.543)	0.993 (0.796)	0.999 (0.977)	0.991 (0.586)
I / σI	71.43 (3.56)	43.97 (2.64)	17.03 (2.90)	22.78 (9.66)	9.75 (2.49)
Completeness (%)	99.98 (99.98)	96.97 (99.15)	99.92 (99.90)	98.25 (99.33)	99.90 (99.93)
Redundancy	31.3 (25.0)	12.9 (11.0)	6.8 (4.7)	7.0 (6.8)	7.2 (7.3)

Refinement
Resolution (Å)	54.31–1.58 (1.64–1.58)	46.09–1.98 (2.05–1.98)	46.7–1.99 (2.06–1.99)	43.72–1.98 (2.05–1.98)	41.04–1.99 (2.06–1.99)
No. reflections	115039 (11360)	59886 (6056)	59677 (5857)	59416 (5901)	58990 (5831)
R_work/R_free	0.165/0.189 (0.199/0.248)	0.202/0.255 (0.264/0.340)	0.184/0.219 (0.239/0.293)	0.222/0.271 (0.225/0.281)	0.192/0.228 (0.332/0.391)
No. atoms	5961	4627	5412	5468	5453
Protein	4636	4627	4639	4661	4590
Duplex	490	469	487	429	475
Solvent	835	546	286	378	388
B-factors	26.73	42.07	45.96	42.25	39.05
Protein	25.11	42.17	45.39	41.74	38.85
Duplex/dAMPNPP	40.11	55.17	117.16	101.56/106.4	60.07
Solvent	36.64	40.95	46.01	41.13	41.37
R.m.s deviations
Bond lengths (Å)	0.006	0.007	0.008	0.008	0.007
Bond angles (°)	0.82	0.89	0.84	1.15	0.85

^*Values in parentheses are for the highest-resolution shell.

elife-41604-v2.xml

10.7554/eLife.41604.012

Table 4.Data collection and refinement statistics.

Data collection	∆N∆C-IDFP·1 Complex (PDB entry 6MVD)
Space group	C2
Cell dimensions a, b, c (Å) α, β, γ (°)	134.5, 106.7, 117.8 90.0, 125.5, 90.0
Resolution (Å)	30.0–3.10 (3.15–3.10)^*
R_merge	0.115 (≥1)
I / σ_I	11.1 (1.27)
Completeness (%)	98.9 (100.0)
Redundancy	4.2 (4.2)
CC_1/2	(0.55)
Refinement
Resolution (Å)	28.8–3.10
No. reflections	20,413
R_work/R_free	19.3/23.9
Number of atoms Protein Ligand Water	6182 5978 183 20
B-factors (Å²) Overall Protein Ligand Water	73.6 73.2 91.4 41.1
R.m.s. deviations Bond lengths (Å) Bond angles (°)	0.008 1.33
Ramachandran statistics Favored Allowed Outliers	93.5 6.0 0.5
MolProbity score	2.19
Clashscore, all atoms	4.4

^*Values in parentheses are for the highest-resolution shell.

elife-43204-v1.xml

10.7554/eLife.43204.006

Table 1.Data collection and refinement statistics.

	Pol I (core) EC + GMPCPP	Pol I EC + GMPCPP	Pol I* EC + GMPCPP	Apo Pol I*
Data collection
Particle number	54,017	30,232	182,488	73,660
Pixel size (Å/pix)	1.04	1.04	1.04	1.04
Average resolution (Å)	3.18	3.42	3.18	3.21
B-factor	−44.5	−34.2	−92.9	−99.6
EMDB code	EMD-0240	EMD-0238	EMD-0239	EMD-0241
Refinement statistics*
PDB code	6HLR	6HKO	6HLQ	6HLS
CC (atoms)^†	0.816	0.804	0.796	0.797
RMSD (bonds)	0.007	0.006	0.006	0.007
RMSD (angles)	1.22	1.18	1.18	1.25
Clashscore	4.74	5.27	5.13	5.17
Rotamer outliers (%)	0.12	0.14	0.09	0.32
C-beta deviations (%)	0	0	0	0
Ramachandran plot
Outliers (%)	0	0	0	0
Allowed (%)	4.9	5.64	4.59	5.48
Favored (%)	95.1	94.36	95.41	94.61
Molprobity score	1.58	1.67	1.59	1.65

*Calculated with Molprobity.

†From PHENIX real space refinement.

elife-43676-v2.xml

10.7554/eLife.43676.012

Table 2.Data collection and refinement statistics.

	SETD3–β-actin	SETD3-methylated β-actin
Protein Data Bank ID	6ICV	6ICT
Data collection
Radiation wavelength (Å)	0.9789	0.9792
Space group	P 1 21 1	P 1 21 1
Cell dimensions
a, b, c (Å)	60.19, 175.17, 66.50	59.98, 176.69, 125.89
α, β, γ (°)	90, 92.57, 90	90, 93.37, 90
Resolution (Å)	35.00–2.15 (2.23–2.15)	72.27–1.95 (2.06–1.95)
R_merge	0.135 (0.609)	0.169 (0.868)
I / σI	14 (3.4)	8.1 (2.6)
CC1/2	0.988 (0.884)	0.991 (0.827)
Completeness (%)	100(100)	99.1 (99.7)
Redundancy	6.4 (6.4)	7.0 (7.0)
Refinement
Resolution (Å)	35.00–2.15	59.87–1.95
No. of reflections (used/free)	71998/3629	187163/9084
R_work/R_free	0.168/0.205	0.178/0.214
Number of atoms/B-factor (Å²)	8493/30.7	16956/33.7
Protein	7574/30.3	15147/33.1
Peptide	276/32.9	591/38.4
AdoHcy	52/19.3	104/20.0
Solvent	591/36.2	1114/40.0
RMSD bonds (Å)/angles (°)	0.007/0.84	0.007/0.87
Ramachandran Plot favored/allowed/outliers (%)	98.76/1.24/0	98.98/1.02/0

Values in parentheses are for the highest-resolution shell.

elife-43676-v3.xml

10.7554/eLife.43676.012

Table 2.Data collection and refinement statistics.

	SETD3–β-actin	SETD3-methylated β-actin
Protein Data Bank ID	6ICV	6ICT
Data collection
Radiation wavelength (Å)	0.9789	0.9792
Space group	P 1 21 1	P 1 21 1
Cell dimensions
a, b, c (Å)	60.19, 175.17, 66.50	59.98, 176.69, 125.89
α, β, γ (°)	90, 92.57, 90	90, 93.37, 90
Resolution (Å)	35.00–2.15 (2.23–2.15)	72.27–1.95 (2.06–1.95)
R_merge	0.135 (0.609)	0.169 (0.868)
I / σI	14 (3.4)	8.1 (2.6)
CC1/2	0.988 (0.884)	0.991 (0.827)
Completeness (%)	100(100)	99.1 (99.7)
Redundancy	6.4 (6.4)	7.0 (7.0)
Refinement
Resolution (Å)	35.00–2.15	59.87–1.95
No. of reflections (used/free)	71998/3629	187163/9084
R_work/R_free	0.168/0.205	0.178/0.214
Number of atoms/B-factor (Å²)	8493/30.7	16956/33.7
Protein	7574/30.3	15147/33.1
Peptide	276/32.9	591/38.4
AdoHcy	52/19.3	104/20.0
Solvent	591/36.2	1114/40.0
RMSD bonds (Å)/angles (°)	0.007/0.84	0.007/0.87
Ramachandran Plot favored/allowed/outliers (%)	98.76/1.24/0	98.98/1.02/0

Values in parentheses are for the highest-resolution shell.

elife-43788-v2.xml

10.7554/eLife.43788.003

Table 1.Data collection and refinement statistics

Protein:RNA		PUF-8: PBE	FBF-2 SS/Y: PBE	FBF-2 AS/Y: PBE	FBF-2 AQ/Y: PBE
Data collection
Space group		C2	P61	P61	P61
Unit Cell	a, b, c (Å)	109.2, 189.0, 63.2	96.4, 96.4, 99.9	96.5, 96.5, 101.1	95.9, 95.9, 100.4
Unit Cell	α, β, γ (°)	90, 103.6, 90	90, 90, 120	90, 90, 120	90, 90, 120
Resolution (Å)		50–2.55 (2.59–2.55)^*	50–2.25 (2.29–2.25)^*	50–2.25 (2.33–2.25)^*	50–2.85 (2.9–2.85)^*
R_sym or R_merge		0.191 (0.692)	0.101 (0.704)	0.104 (0.772)	0.191 (0.957)
I /σI		9.4 (1.9)	19.2 (3.42)	17.1 (2.98)	12.8 (2.34)
Completeness (%)		98.9 (98.0)	99.9 (100)	99.9 (100)	99.6 (99.2)
Redundancy		6.9 (3.6)	5.7 (5.7)	5.7 (5.7)	10.7 (8.8)

Refinement
Resolution (Å)		33.8–2.6	32.0–2.3	31.6–2.3	27.5–2.9
No. reflections		37,625	25,089	25,386	12,185
R_work/R_free		0.229/ 0.285	0.158/ 0.204	0.167/ 0.223	0.219/ 0.272
No. atoms
Protein		8415	3197	3194	3189
RNA		507	150	168	168
Solvent		229	169	109	21
B-factors (Å²)
Wilson B		29.7	36.6	35.5	48.4
Protein		32.8	45.3	45.1	50.2
RNA		43.6	51.4	58.8	64.8
Solvent		32.7	49.6	44.3	23.1
R.m.s deviations
Bond lengths (Å)		0.002	0.007	0.007	0.002
Bond angles (°)		0.45	0.77	0.78	0.38

^*Values in parentheses are for the highest-resolution shell.

elife-43788-v3.xml

10.7554/eLife.43788.003

Table 1.Data collection and refinement statistics

Protein:RNA		PUF-8: PBE	FBF-2 SS/Y: PBE	FBF-2 AS/Y: PBE	FBF-2 AQ/Y: PBE
Data collection
Space group		C2	P61	P61	P61
Unit Cell	a, b, c (Å)	109.2, 189.0, 63.2	96.4, 96.4, 99.9	96.5, 96.5, 101.1	95.9, 95.9, 100.4
Unit Cell	α, β, γ (°)	90, 103.6, 90	90, 90, 120	90, 90, 120	90, 90, 120
Resolution (Å)		50–2.55 (2.59–2.55)^*	50–2.25 (2.29–2.25)^*	50–2.25 (2.33–2.25)^*	50–2.85 (2.9–2.85)^*
R_sym or R_merge		0.191 (0.692)	0.101 (0.704)	0.104 (0.772)	0.191 (0.957)
I /σI		9.4 (1.9)	19.2 (3.42)	17.1 (2.98)	12.8 (2.34)
Completeness (%)		98.9 (98.0)	99.9 (100)	99.9 (100)	99.6 (99.2)
Redundancy		6.9 (3.6)	5.7 (5.7)	5.7 (5.7)	10.7 (8.8)

Refinement
Resolution (Å)		33.8–2.6	32.0–2.3	31.6–2.3	27.5–2.9
No. reflections		37,625	25,089	25,386	12,185
R_work/R_free		0.229/ 0.285	0.158/ 0.204	0.167/ 0.223	0.219/ 0.272
No. atoms
Protein		8415	3197	3194	3189
RNA		507	150	168	168
Solvent		229	169	109	21
B-factors (Å²)
Wilson B		29.7	36.6	35.5	48.4
Protein		32.8	45.3	45.1	50.2
RNA		43.6	51.4	58.8	64.8
Solvent		32.7	49.6	44.3	23.1
R.m.s deviations
Bond lengths (Å)		0.002	0.007	0.007	0.002
Bond angles (°)		0.45	0.77	0.78	0.38

^*Values in parentheses are for the highest-resolution shell.

elife-44199-v1.xml

10.7554/eLife.44199.007

Table 1.Data collection and refinement statistics.

Datasets:	High-resolution (remote)	Se SAD phasing (peak)
Data collection
Beamline	APS 23ID-D	APS 23ID-D
Wavelength (Å)	1.0332	0.9793
Space group	P2₁2₁2₁	P2₁2₁2₁
Cell dimensions a, b, c (Å) α, β, γ (°)	49.73, 56.58, 173.88 90, 90, 90	49.63, 56.46, 173.87 90, 90, 90
Resolution (Å)	37.74–1.90 (1.94–1.90)	49.63–2.50 (2.60–2.50)
Total reflections	159936 (10248)	175374 (20071)
Unique reflections	39302 (2495)	17561 (1930)
Multiplicity	4.1 (4.1)	10.0 (10.4)
Completeness (%)	99.3 (99.1)	99.1 (98.1)
I/σ(I)	10.3 (1.2)	21.9 (7.3)
CC(1/2)	0.998 (0.793)	0.999 (0.982)
R_pim	0.036 (0.575)	0.024 (0.090)
Phasing
Number of Se sites		2
Figure of merit		0.64
Refinement
R_work/R_free	0.170/0.214
Number of atoms	3457
Wilson B factor (Å)	33.8
RMS deviations Bonds (Å) Angles (°)	0.007 1.386
Ramachandran plot % favored % allowed % outliers	97.91 1.83 0
PDB ID	6N67

Values in parentheses refer to the highest resolution shell.

The R_free set consists of 5% randomly chosen data excluded from refinement.

elife-45221-v2.xml

10.7554/eLife.45221.012

Table 2.Data collection and refinement statistics.

	HDVD mCST-CMP			LCP mCST∆C
	Native	Hg	Pt	CMP	CMP-Sia
Data collection
Space group	P2₁	P2₁	P2₁	C2	C2
Crystals (#)	5	1	1	26	1
Cell dimensions (Å)
a	51.82	51.88	51.50	50.15	50.42
b	193.96	194.00	193.46	49.53	50.12
c	66.44	66.89	66.31	137.9	132.33
α, γ = 90; β = (°)	101.79	102.16	101.63	92.65	91.83
Resolution (Å)	49–3.4 × 3.4 × 4.6^* (3.47–3.38)	49–3.5 × 3.5 × 5.6^† (3.59–3.50)	49–4.2 × 4.2 × 7.6^† (4.31–4.20)	47–2.58 (2.65–2.58)	48–2.75 (2.83–2.75)
R_merge	0.07 (0.95)	0.14 (4.03)	0.23 (2.62)	0.14 (0.47)	0.13 (1.37)
R_pim	0.03 (0.67)	0.09 (2.43)	0.14 (1.63)	0.05 (0.28)	0.07 (0.75)
I / σI	6.7 (1.6)	6.8 (0.5)	4.9 (0.7)	9.3 (2.2)	6.0 (1.0)
CC_1/2 in outer shell	0.65	0.20	0.30	0.79	0.41
Completeness (%)	67.3 (4.0)^*	99.0 (99.6)	99.9 (100)	97.8 (79.1)^‡	99.8 (99.4)
Redundancy	3.6 (2.2)	7.1 (7.4)	6.8 (7.0)	7.2 (3.3)	4.1 (4.3)
MIRAS phasing^§
Phasing power (iso/ano)		2.39/1.16	1.47/0.29
R_cullis (iso/ano)		0.45/0.44	0.65/1.00
Figure of merit (SHARP)		0.31
Figure of merit (DM)		0.89
Refinement
Resolution (Å)	49–3.4 (3.50–3.38)			47–2.58 (2.67–2.58)	48–2.75 (2.85–2.75)
No. reflections (No. in free set)	11456 (573)			10101 (514)	8305 (404)
R_work/R_free	28.9/32.1^¶ (64.9/63.0)^**			24.1/25.2 (26.3/33.6)	25.6/27.9 (37.5/37.8)
No. atoms
Protein	4502			2235	2244
Ligand	42			21	41
Water	0			11	3
B-factors
Protein	149.4			47.8	81.1
Ligand	122.1			39.4	90.6
Water	—			42.8	58.9
R.m.s. deviations
Bond lengths (Å)	0.007			0.008	0.007
Bond angles (°)	1.011			1.127	1.031

*The diffraction data are anisotropic. For phasing and model refinement, the data were anisotropically truncated and B-factor sharpened as described in the Methods section. The data collection and refinement statistics reflect this. The dataset was overall 94.7% (81.7% in high-resolution shell) complete before being truncated. For the truncated dataset, resolution shells up to 4.4 Å are at least 95% complete.

^†The diffraction data are anisotropic; however, the datasets were left unmodified for phasing.

^‡The lower completeness for the high-resolution shell is due to only a minority of the crystals diffracting to ~2.6 Å. Most of the crystals only diffracted to ~2.7 Å, as evidenced by the 2.72–2.65 Å shell being 98.8% complete.

^§The acentric phasing power and R_cullis for the isomorphous (iso) and anomalous (ano) signals are shown. Phase figure of merits are also shown after refinement in SHARP and after density modification with DM.

^¶The refinement statistics in this column represent the model from the LCP mCST∆C-CMP crystal being refined against the native HDVD mCST-CMP dataset.

**R-factors in the 3.81–3.64 Å and 4.26–4.01 Å shells, which are 34% and 79% complete, respectively, are 38.5/39.8% and 31.2/34.4% (R_work/R_free), respectively.

Values in parentheses are for the highest-resolution shell, unless otherwise indicated.

elife-45221-v3.xml

10.7554/eLife.45221.012

Table 2.Data collection and refinement statistics.

	HDVD mCST-CMP			LCP mCST∆C
	Native	Hg	Pt	CMP	CMP-Sia
Data collection
Space group	P2₁	P2₁	P2₁	C2	C2
Crystals (#)	5	1	1	26	1
Cell dimensions (Å)
a	51.82	51.88	51.50	50.15	50.42
b	193.96	194.00	193.46	49.53	50.12
c	66.44	66.89	66.31	137.9	132.33
α, γ = 90; β = (°)	101.79	102.16	101.63	92.65	91.83
Resolution (Å)	49–3.4 × 3.4 × 4.6^* (3.47–3.38)	49–3.5 × 3.5 × 5.6^† (3.59–3.50)	49–4.2 × 4.2 × 7.6^† (4.31–4.20)	47–2.58 (2.65–2.58)	48–2.75 (2.83–2.75)
R_merge	0.07 (0.95)	0.14 (4.03)	0.23 (2.62)	0.14 (0.47)	0.13 (1.37)
R_pim	0.03 (0.67)	0.09 (2.43)	0.14 (1.63)	0.05 (0.28)	0.07 (0.75)
I / σI	6.7 (1.6)	6.8 (0.5)	4.9 (0.7)	9.3 (2.2)	6.0 (1.0)
CC_1/2 in outer shell	0.65	0.20	0.30	0.79	0.41
Completeness (%)	67.3 (4.0)^*	99.0 (99.6)	99.9 (100)	97.8 (79.1)^‡	99.8 (99.4)
Redundancy	3.6 (2.2)	7.1 (7.4)	6.8 (7.0)	7.2 (3.3)	4.1 (4.3)
MIRAS phasing^§
Phasing power (iso/ano)		2.39/1.16	1.47/0.29
R_cullis (iso/ano)		0.45/0.44	0.65/1.00
Figure of merit (SHARP)		0.31
Figure of merit (DM)		0.89
Refinement
Resolution (Å)	49–3.4 (3.50–3.38)			47–2.58 (2.67–2.58)	48–2.75 (2.85–2.75)
No. reflections (No. in free set)	11456 (573)			10101 (514)	8305 (404)
R_work/R_free	28.9/32.1^¶ (64.9/63.0)^**			24.1/25.2 (26.3/33.6)	25.6/27.9 (37.5/37.8)
No. atoms
Protein	4502			2235	2244
Ligand	42			21	41
Water	0			11	3
B-factors
Protein	149.4			47.8	81.1
Ligand	122.1			39.4	90.6
Water	—			42.8	58.9
R.m.s. deviations
Bond lengths (Å)	0.007			0.008	0.007
Bond angles (°)	1.011			1.127	1.031

^†The diffraction data are anisotropic; however, the datasets were left unmodified for phasing.

^¶The refinement statistics in this column represent the model from the LCP mCST∆C-CMP crystal being refined against the native HDVD mCST-CMP dataset.

**R-factors in the 3.81–3.64 Å and 4.26–4.01 Å shells, which are 34% and 79% complete, respectively, are 38.5/39.8% and 31.2/34.4% (R_work/R_free), respectively.

Values in parentheses are for the highest-resolution shell, unless otherwise indicated.

elife-45286-v2.xml

10.7554/eLife.45286.009

Table 2.Data collection and refinement statistics.

	Glt_Tk D-Asp
Data collection
Space group	P3221
Cell dimensions
a, b, c (Å)	116.55, 116.55, 314.77
α, β, γ (°)	90.00, 90.00 120.00
Resolution (Å)	48.06-2.80 (2.87-2.80)*
R_meas	0.11 (>1)
CC_1/2	99.9 (11.7)
I / σI	8.40 (0.98)
Completeness (%)	99.3 (98.9)
Redundancy	5 (4)
Refinement
Resolution (Å)	2.80
No. reflections	301,077
R_work/R_free (%)s	23.4/27.2
No. of atom
Protein	9262
PEG/detergent	181/33
Ligand/ion	27/9
Water	-
B-factors
Protein	127
PEG/detergent	147/174
Ligand/ion	114/117
Water	-
R.m.s. deviations
Bond lengths (Å)	0.008
Bond angles (°)	1.162

^*Values in parentheses are for the highest-resolution shell.

elife-45779-v2.xml

10.7554/eLife.45779.010

Table 1.Data collection and refinement statistics

Data collection and processing	TRPV2_RTx-ND	TRPV2_{RTx-APOL 1}	TRPV2_{RTx-APOL 2}	TRPV2_{RTx-APOL 3}
Electron microscope	Titan Krios	Titan Krios
Electron detector	Falcon III	Falcon III
Magnification	75,000x	75,000x
Voltage (kV)	300	300
Electron exposure (e–/Å²)	42	42
Defocus range (μm)	−1.25 to −3.0	−1.25 to −3.0
Pixel size (Å)	1.08	1.08
Detector	Counting	Counting
Total extracted particles (no.)	1,407,292	580,746
Refined particles (no.)	482,602	470,760
Reconstruction
Final particles (no.)	112,622	101,570	109,623	90,862
Symmetry imposed	C2	C4	C2	C2
Nominal Resolution (Å)	3.8	2.9	3.3	4.19
FSC 0.143 (masked/unmasked)	3.7/3.9	2.9/3.05	3.2/3.5	4.0/4.3
Map sharpening B factor (Å²)	−30	−78	−92	−133
Refinement
Model composition Non-hydrogen atoms Protein residues Ligands	16,878 2396 RTx: 4	18,236 2404 RTx: 4	18,452 2440 RTx: 4	17,548 2440 RTx: 4
Validation MolProbity score Clashscore Poor rotamers (%)	1.39 4 0	1.11 1.9 0	1.28 2.7 0	1.37 2.7 0
Ramachandran plot
Favored (%) Allowed (%) Disallowed (%)	96.5 3.5 0	97.1 2.9 0	96.6 3.4 0	95.5 4.5 0

elife-47701-v1.xml

10.7554/eLife.47701.007

Table 1.Data collection and refinement statistics.

	Y799W(K⁺)E2-MgF_x	Y799W(Rb⁺)E2-MgF_x	Y799W(Rb⁺)E2-AlF_x	WT(Rb⁺)E2-MgF_x
Data collection
Resolution (Å)^†	2.7 × 2.8 × 2.5 (2.6–2.5)^‡	2.8 × 2.8 × 2.6 (2.7–2.6)	2.8 × 3.0 × 2.5 (2.6–2.5)	5.1 × 5.1 × 4.3 (4.5–4.3)
Space group	P 3₁ 2 1	P 3₁ 2 1	P 3₁ 2 1	C 1 2 1
Cell dimensions
a, b, c (Å)	103.37, 103.37, 370.01	103.38, 103.38, 369.86	103.23, 103.23, 369.44	191.51, 106.43, 250.96
α, β, γ (°)	90, 90, 120	90, 90, 120	90, 90, 120	90, 107.79, 90
R_merge	0.067 (3.685)	0.080 (2.248)	0.106 (3.499)	0.152 (1.359)
R_pim	0.022 (1.179)	0.030 (0.855)	0.040 (1.295)	0.065 (0.544)
I/σI	20.18 (0.93)	16.19 (1.16)	11.64 (0.77)	7.19 (0.92)
C/C1/2	0.99 (0.59)	0.99 (0.70)	0.99 (0.60)	0.99 (0.75)
Completeness (%)	85.65 (26.79)	88.93 (36.11)	76.00 (18.98)	94.94 (53.46)
Redundancy	10.2 (10.6)	8.0 (7.8)	8.0 (8.2)	6.6 (7.2)
Refinement
Resolution (Å)	48–2.5 (2.6–2.5)	48–2.6 (2.7–2.6)	50–2.5 (2.6–2.5)	48–4.3 (4.5–4.3)
No. of reflections	69,037 (2135)	63,831 (2533)	61,013 (1502)	31,390 (1747)
R_work/R_free (%)	20.1/25.7 (37.3/48.0)	20.6/26.2 (35.1/43.5)	21.5/27.4 (32.7/42.6)	26.3/33.9 (33.4/41.2)
Wilson B-factor	60.74	52.60	48.43	158.52
No. of atoms	10,513	10,485	10,498	19,823
Protein	9736	9762	9763	19,623
Ligands	362	362	364	200
Average B-factor	74.40	62.68	60.03	244.07
Protein (Å²)	72.62	60.98	57.83	243.40
Ligands (Å²)	122.80	114.14	103.16	310.29
R.m.s deviations
Bond lengths (Å)	0.010	0.009	0.010	0.005
Bond angles (°)	1.36	1.51	1.39	1.18

^†The diffraction data are anisotropic. The resolution limits given are for the a*, b* and c* axes, respectively.

^‡Statistics for the highest-resolution shell are shown in parentheses.

elife-47713-v2.xml

10.7554/eLife.47713.019

Table 1.Data collection and refinement statistics

	Pikp^NK-KE–AVR-PikD	Pikp^NK-KE–AVR-PikE
Data collection statistics
Wavelength (Å)	0.9763	0.9763
Space group	P 2₁ 2₁ 2₁	P 2₁ 2₁ 2₁
Cell dimensions
a, b, c (Å)	29.79, 65.33, 75.86	66.46, 80.70, 105.58
Resolution (Å)^*	32.80–1.60 (1.63–1.60)	29.50–1.85 (1.89–1.85)
R_merge (%)^#	8.1 (97.1)	5.2 (75.1)
I/σI^#	16.1 (2.6)	31.0 (4.1)
Completeness (%)^#	100 (100)	99.8 (97.8)
Unique reflections^#	20,294 (978)	49337 (2963)
Redundancy^#	12.8 (13.3)	18.3 (17.8)
CC^(1/2) (%)^#	99.9 (86.6)	100 (95.2)
Refinement and model statistics
Resolution (Å)	32.82–1.60 (1.64–1.60)	29.52–1.85 (1.90–1.85)
R_work/R_free (%)^{^}	19.7/23.2 (25.5/27.3)	18.6/23.0 (29.1/35.0)
No. atoms (Protein)	1277	3604
B-factors (Protein)	25.6	39.7
R.m.s. deviations^{^}
Bond lengths (Å)	0.009	0.012
Bond angles (°)	1.5	1.4
Ramachandran plot (%)**
Favored	98.1	97.3
Outliers	0	0.2
MolProbity Score	1.41 (93^th percentile)	1.59 (91^st percentile)

^*The highest resolution shell is shown in parenthesis.

^#As calculated by Aimless, ^{^}As calculated by Refmac5, **As calculated by MolProbity.

elife-50155-v1.xml

Table 1.Data collection and refinement statistics.

	Native T₂R-TTL-AlF₃ (PDB 6s9e)	Native T₂R-TTL-BeF₃^- (PDB 6gze)
Data collection
Space group	P2₁2₁2₁	P2₁2₁2₁
Cell dimensions
a, b, c (Å)	104.999, 157.357, 180.261	104.176, 156.744, 180.587
α, β, γ (°)	90.00, 90.00, 90.00	90.00, 90.00, 90.00
Resolution (Å)	48.003–2.25	49.458–2.49
R_merge	0.075 (1.222)	0.071 (1.159)
R_pim	0.025 (0.417)	0.028 (0.473)
I/σI	16.5 (1.8)	7.1 (0.6)
Completeness (%)	99.0 (99.0)	100 (100)
Redundancy	9.6 (9.2)	7.1 (7.0)
CC_half	0.979 (0.635)	0.999 (0.993)
Refinement
Resolution (Å)	48.003–2.25	49.458–2.49
No. of reflections	140102	103915
R_work/R_free	0.2029/0.2278	0.2121/0.2565
No. of atoms	17701	16799
Protein	17279	16572
Ligand	223	175
Water	199	52
B-factors
Protein	64.0	80.4
Ligand	59.5	73.0
Water	45.7	67.5
Wilson B	48.90	64.70
r.m.s deviation
Bond lengths (Å)	0.002	0.003
Bond angles (°)	0.526	0.557
Ramachandran %
Favor/allow/out	97.88/2.12/0.00	97.52/2.48/0.00

^*Data were collected from a single crystal.

^**Values in parentheses are for the highest resolution shell.

elife-50661-v2.xml

Table 1.Data collection and refinement statistics.

Data collection statistics
PDB ID	6S2J	6S5B	6S5D	6S7R
Crystal	R16K_ATP	R16K_ADP	R16A_ATP	R16A_ADP
Space group	I4	P2₁2₁2₁	I4	P1
Unit-cell dimensions a, b, c (Å) α, β, γ (°)	123.3, 123.3, 84.4 90, 90, 90	85.8, 137.4, 202.6 90, 90, 90	121.6, 121.6, 83.7 90, 90, 90	93.0, 97.9, 144.6 90.4, 97.1, 110.3
Protomers in the asymmetric unit	2	8	2	16
Wavelength (Å)	0.954240	0.979480	0.978570	0.978570
Resolution (Å)	46.16–2.67 (2.80–2.67)	49.51–3.05 (3.16–3.05)	45.60–3.39 (3.66–3.39)	48.80–3.73 (3.86–3.73)
No. of reflections (measured/unique)	85203/17872	383771/46032	76213/8535	161349/46426
Multiplicity	4.8 (4.5)	8.3 (4.2)	8.9 (8.5)	3.5 (3.0)
Completeness (%)	99.0 (96.5)	99.2 (91.6)	99.8 (99.0)	94.0 (51.2)
Rmerge (all I) (%)	5.5 (86.8)	14.8 (47.4)	4.7 (182.9)	9.5 (96.6)
Rmeasure (all I) (%)	6.2 (98.1)	15.8 (53.8)	5.0 (194.6)	11.2 (116.0)
Mean I / σ(I)	13.9 (1.7)	15.9 (0.2)	17.1 (1.3)	7.4 (1.1)
CC_1/2	0.999 (0.541)	0.995 (0.886)	1.000 (0.573)	0.996 (0.494)
Refinement statistics
Resolution range (Å)	46.16–2.67	48.17–3.05	45.60–3.39	48.80–3.73
R_work/R_free (%)	18.96/23.57	20.93/24.29	23.83/27.90	24.57/30.04
No. of reflections	17870	46032	8535	46426
Total No. of atoms	6969	13784	3459	25028
No. of waters	2	-	2	-
No. of ATP	2	-	2	-
No. of ADP	-	8	-	16
No. of Mg	1	-	1	-
Wilson B factor(Å²)	90.2	97.4	194.2	152.9
r.m.s.d. bond lengths (Å)	0.013	0.003	0.003	0.003
r.m.s.d. bond angles (°)	1.086	0.760	0.745	0.824
Ramachandran plot
Residues in favored/allowed regions (%)	98/2	99/1	97/3	98/2
Data collection statistics
Crystal	E125Q_ATP	E125Q_ADP	A80P_ATP	A80P_ADP
PDB ID	6S5N	6S5O	6S5E	6S5G
Space group	C222₁	C222₁	P2₁2₁2₁	P2₁2₁2₁
Unit-cell dimensions a, b, c (Å) α, β, γ (°)	109.1, 156.5, 286.4 90, 90, 90	108.2, 155.2, 285.9 90, 90, 90	85.7, 133.9, 205.1 90, 90, 90	85.3, 132.9, 203.3 90, 90, 90
Protomers in the asymmetric unit	8	8	8	8
Wavelength (Å)	0.978570	0.978570	0.978570	0.978570
Resolution (Å)	48.24–4.09 (4.48–4.09)	48.07–3.98 (4.36–3.98)	49.63–3.89 (4.20–3.89)	49.28–4.33 (4.84–4.33)
No. of reflections (measured/unique)	131430/19704	274868/20970	146620/22230	100662/14674
Multiplicity	6.7 (6.8)	13.1 (13.0)	6.6 (6.6)	6.9 (4.7)
Completeness (%)	99.5 (98.3)	99.4 (97.9)	99.5 (98.0)	91.9 (79.1)
Rmerge (all I) (%)	12.7 (113.5)	11.2 (132.6)	8.1 (133.9)	19.1 (56.8)
Rmeasure (all I) (%)	13.7 (122.9)	11.7 (138.1)	8.8 (145.4)	20.5 (62.9)
Mean I / σ(I)	9.5 (1.7)	12.0 (1.9)	10.3 (1.3)	7.9 (2.6)
CC_1/2	0.999 (0.835)	0.999 (0.771)	0.999 (0.830)	0.995 (0.873)
Refinement statistics
Resolution range (Å)	48.24–4.09	47.66–3.98	47.88–3.89	49.28–4.33
R_work/R_free (%)	27.91/31.99	24.96/28.62	26.02/31.72	25.37/31.43
No. of reflections	19704	20970	22230	14674
Total No. of atoms	12594	12426	13912	13744
No. of waters	-	-	-	-
No. of ATP	8	-	8	-
No. of ADP	-	8	-	8
No. of Mg	-	-	-	-
Wilson B factor(Å²)	183.9	201.8	188.6	135.7
r.m.s.d. bond lengths (Å)	0.003	0.003	0.003	0.003
r.m.s.d. bond angles (°)	0.804	0.791	0.883	0.729
Ramachandran plot
Residues in favored/allowed regions (%)	98/2	97/3	98/2	97/3
Data collection statistics
Crystal	WT_ATP_Ca
PDB ID	6S5C
Space group	I4
Unit-cell dimensions a, b, c (Å) α, β, γ (°)	122.7, 122.7, 84.0 90, 90, 90
Protomers in the asymmetric unit	2
Wavelength (Å)	0.978570
Resolution (Å)	45.94–3.00 (3.18–3.00)
No. of reflections (measured/unique)	123606/12614
Multiplicity	9.8 (9.8)
Completeness (%)	99.8 (98.9)
Rmerge (all I) (%)	4.3 (141.8)
Rmeasure (all I) (%)	4.6 (149.6)
Mean I / σ(I)	24.5 (1.6)
CC_1/2	0.999 (0.658)
Refinement statistics
Resolution range (Å)	37.81–3.00
R_work/R_free (%)	20.70/25.88
No. of reflections	12614
Total No. of atoms	3475
No. of waters	-
No. of ATP	2
No. of ADP	-
No. of Ca	1
Wilson B factor(Å²)	135.1
r.m.s.d. bond lengths (Å)	0.004
r.m.s.d. bond angles (°)	0.697
Ramachandran plot
Residues in favored/allowed regions (%)	98/2

Rmsd: root-mean-square deviation; values in parenthesis correspond to the highest resolution shell.

elife-52983-v2.xml

Table 1.Data collection and refinement statistics.

Collection parameters for initial test data set and void peak analysis on the Talos Arctica and final collection on Titan Krios microscopes. Refinement details for initial model, consensus map, and focused refinements.

Data Collection
Collection	Initial Screening	Collection 1	Collection 2	Void peak
Microscope	Talos Arctica	Titan Krios	Titan Krios	Talos Arctica
Voltage (kV)	200	300	300	200
Detector	Gatan K2	Gatan K2	Gatan K2	Gatan K3
Pixel size (Å/pixel)	1.14	0.82	0.82	0.9
Exposure Time (s)	9	10	10	11.7
Electron dose (e-/Å²)	63	80	67	58
Defocus range (µm)	1.5-2.5	0.4-1.2	0.6-1.4	1.5-2.5
Number of micrographs	2,499	2,705	4,632	1,215
Consensus Reconstruction
Data Set	Initial Screening	Collection 1 & 2		Void peak
Software	Relion 2.1, cisTEM, and cryosparc	Relion 3.0		cisTEM
# of particles, picked	240,000	778,149		259,333
# of particles post, Class2D	138,000	554,901		640
# of particles post, Class3D	46,830	362,438		NA
# of particles post, skip align Class3D	NA	90,479		NA
Symmetry	C1	C1		NA
Map sharpening B-factor (Å²)	NA	-160		NA
Final resolution (Å)	4.7 Å	4.0 Å		NA
Focused Refinements
Location of focus	# of particles	Resolution
Protomer i	76,967	3.8
Protomer ii	90,479	3.8
Symmetry expanded protomer	52,067	3.7
Periplasmic EccB3	70,000	5.8
ATPase 1, 2, and 3	30,000	7

elife-55966-v2.xml

Table 2.Data collection and refinement statistics.

	B56:KIF4A_LE,PE^*,†	B56:AIM1^*,‡
PDB Data collection	6OYL	6VRO
Space group	P 2₁ 2₁ 2₁	I4
Cell dimensions
a, b, c (Å)	53.3, 108.0, 117.8	111.0, 111.0, 108.9
Α, β, γ(°)	90, 90, 90	90, 90, 90
Resolution (Å)	39.52–3.15	39.26–2.45
R_merge	0.100 (1.104)	0.091 (1.721)
Mean I /σI	11.5 (1.8)	12.4 (1.2)
Completeness (%)	96.6 (83.1)	99.8 (99.4)
Multiplicity	8.2 (7.7)	7.0 (7.0)
CC_1/2	0.999 (0.730)	0.999 (0.673)

Refinement
Resolution (Å)	39.52–3.15 (3.26–3.15)	38.88–2.45 (2.54–2.45)
No. reflections	11868	24208
R_work/R_free	0.22 (0.36)/0.24 (0.41)	0.22 (0.33)/0.23 (0.38)
No. atoms
Protein	2796	2777
Water	7	36
B-factors
Protein	66.4	70.1
Water	60.4	62.1
RMS deviations
Bond lengths (Å)	0.002	0.002
Bond angles (°)	0.54	0.54
Ramachandran
Outliers (%)	0.3	0.9
Allowed (%)	5.8	3.4
Favored (%)	93.9	95.7
Clashscore	4.3	2.7

^*Data was collected from a single crystal.

^†KIF4A_LE,PE ¹¹⁹²ELKHVATEYQENKAPGKKKKRALASNTSFFSGLEPIEEEPE¹²³².

^‡AIM1 ⁷¹⁶KRKKARMPNSPAPHFAMPPIHEDHLE⁷⁴¹.

^*Values in parentheses are for highest-resolution shell.

elife-58157-v2.xml

Table 1.Data collection and refinement statistics.

	VASH1-SVBP-microtubule
Data collection and processing
Magnification	105,000
Voltage (kV)	300
Electron exposure (e^-Å⁻²)	50
Defocus range (μm)	−0.9 to −2.5
Pixel size (Å)	0.83
Symmetry imposed	Pseudo-Helical
Initial particle images (no.)	156,525
Final particle images (no.)	46,999
Map resolution (Å)/FSC threshold	3.1/0.143
Map sharpening B factor (Å⁻²)	−60
Refinement
Initial model used	PDB: 6OCG, 6DPU
Model resolution (Å)/FSC threshold	3.9/0.5
Model composition
Nonhydrogen atoms	18,196
Protein residues	2296
Ligands	4
B factors (Å⁻²)
Protein	143.68
Ligands	101.97
R.m.s. deviations
Bond lengths (Å)	0.006
Bond angles (°)	0.931
Validation
MolProbity score	1.81
Clashscore	6.2
Poor rotamers (%)	0.36
Ramachandran plot
Favored (%)	92.56
Allowed (%)	7.35
Disallowed (%)	0.09