x-ray data collection and refinement statistics (12)

elife-30395-v2.xml

10.7554/eLife.30395.005

Table 1.X-ray data collection and refinement statistics.

	TFIIA^s-c
Data collection
Space group	P65
Cell dimensions
a, b, c (Å)	123.3, 123.3, 34.8
a, b, g (°)	90, 90, 120
Resolution (Å)	53.4–2.4
Last resolution bin (Å)	2.52–2.38
R_measure (%)	12.9 (64.8)
I / σI	11.5 (2.72)
Completeness (%)	99.8 (99.9)
Multiplicity	6.7 (6.8)
Refinement
Resolution (Å)	40.36–2.38 (2.44–2.38)
No. reflections
Work set	11859
Free set	601
R_work	0.18 (0.27)
R_free	0.24 (0.36)
No. of atoms
Protein	1689
Water	50
r.m.s deviations
Bond lengths (Å)	0.0223
Bond angles (°)	2.088

*Values in parentheses are for highest resolution shell.

elife-33067-v2.xml

10.7554/eLife.33067.005

Table 1.X-ray data collection and refinement statistics

	CrIFT80_1-654 EMP soak	CrIFT80 (fl) native
PDB code		5N4A
Data collection and scaling	Anomalous signal from Hg to ~ 4 Å
Wavelength (Å)	1.0077	1.0000
Resolution range (Å)	50–2.98 (3.13–2.98)	47–1.79 (1.90–1.79)
Space group	P3112	C2221
Unit cell (Å)	a = 139.2 b = 139.2 c = 147.7 α = β = 90 γ = 120.0	a = 82.8 b = 195.4 c = 117.5 α = β = γ = 90.0
Total reflections	1356277 (160974)	718465 (109362)
Unique reflections	33336 (4251)	173548 (27521)
Multiplicity	40.7 (37.9)	6.6 (6.3)
Completeness (%)	99.5 (96.5)	99.5 (97.3)
Mean I/sigma(I)	19.8 (2.8)	11.3 (1.0)
R-merge	0.225 (1.82)	0.095 (1.40)
CC½	0.999 (0.817)	0.998 (0.435)
Refinement
Number of reflections		173479 (27521)
Number of atoms (non-solvent)		5286
Water (solvent)		768
R-work		0.175 (0.324)
R-free		0.208 (0.351)
Ramachandran favoured (%)		97.14
Ramachandran allowed (%)		2.81
Ramachandran outliers (%)		0.15
RMS bonds (Å)		0.0074
RMS angles (°)		1.1
Rotamer outliers (%) Clashscore		1.2 13.2
Average B- Factors (Å²)		28.2

elife-33442-v2.xml

10.7554/eLife.33442.008

Table 1.X-ray data collection and refinement statistics

Data collection and processing
	Native	SeMet 1	SeMet 2	SeMet 1 + 2
Space group	P4₁	P4₁	P4₁	P4₁
Wavelength	0.97793	0.9793	0.9793	0.9793
No. xtals	1	1	1	2
Source	SLS	PETRA	PETRA	PETRA
Detector	Pilatus 6M	Pilatus6M	Pilatus 6M	Pilatus 6M
Mol/AU	2	2	2	2
a,b,c (Å)	87.3 87.3 81.1	88.99 88.99 76.96	89.14 89.14 77.22	88.99 88.99 76.96
α, β, γ (°)	90 90 90	90 90 90	90 90 90	90 90 90
Resolution (Å)	87.3–2.74 (2.81–2.74)*	48.7–3.3 (3.9–3.3)	48.8–3.2 (3.3–3.2)	48.7–3.3 (3.4–3.3)
R_meas	8.2 (155.1)	17.2 (153.4)	18.8 (173.4)	18.7 (167.8)
I/σI	17.3 (1.4)	7.5 (1.1)	7.2 (1.0)	10.4 (1.4)
Completeness (%)	99.8 (98.5)	100.0 (100.0)	99.9 (98.8)	100.0 (100.0)
Redundancy	9.4 (8.7)	7.1 (7.2)	7.0 (6.3)	14.1 (14.1)
Refinement				Phasing
Resolution (Å)	87.3–2.7			FOM 0.39
No. reflections	17103			BAYES-CC 38.1
R_work/R_free(%)	21.6/26.1			12 Selenium-sites
No. atoms:
Protein/ Ligands	3432/6
Water	10
aver. B (Å²)	90.4
R.m.s. deviations
Bond lengths (Å)	0.0076	Ramachandran plot: 98.0% favourable, 0% outliers
Bond angles (°)	1.27

* Values in parentheses are for highest resolution shell

elife-38362-v2.xml

10.7554/eLife.38362.007

Table 1.X-ray data collection and refinement statistics.

Data collection
Data set	KLC1^TPR-JIP1^C-term	KLC1^TPR-TorsinA^C-term
Beam line	P14 (Petra)	I04 (DLS)
Wavelength (Å)	0.9763	0.9795
Resolution range^* (Å)	45.18–2.70 (2.83–2.70)	52.50–2.29 (2.83–2.70)
Space group	C2	C2
Cell dimensions (a, b, c) (Å) (α, β, γ) (°)	107.47, 90.36, 51.70 90, 99.80, 90	106.04, 89.68, 50.99 90, 98.00, 90
Unique reflections^*	13229 (1747)	21275 (1021)
Overall redundancy^*	3.8 (3.9)	4.7 (3.2)
Completeness^* (%)	98.6 (98.5)	99.6 (93.9)
R_merge^* (%)	5.1 (117.6)	8.0 (83.2)
R_p.i.m. (I)^* (%)	4.7 (106.7)	4.0 (52.0)
⟨I/σ(I)⟩^*	11.9 (1.0)	9.0 (1.1)
CC(1/2)^* (%)	99.9 (58.4)	99.7 (74.1)
Refinement
PDB code	6FUZ	6FV0
R_factor (%)	23.3	20.8
R_free (%)	25.6	24.5
# non-H atoms protein water heterogen	3001 13 6 (GOL)	3039 90 7 (PEG)
Average B value (Å²)	113.04	65.81
rms bond lengths (Å)	0.009	0.007
rms bond angles (°)	1.08	0.93

*Numbers in parentheses refer to the highest resolution bin.

elife-38362-v3.xml

10.7554/eLife.38362.007

Table 1.X-ray data collection and refinement statistics.

Data collection
Data set	KLC1^TPR-JIP1^C-term	KLC1^TPR-TorsinA^C-term
Beam line	P14 (Petra)	I04 (DLS)
Wavelength (Å)	0.9763	0.9795
Resolution range^* (Å)	45.18–2.70 (2.83–2.70)	52.50–2.29 (2.83–2.70)
Space group	C2	C2
Cell dimensions (a, b, c) (Å) (α, β, γ) (°)	107.47, 90.36, 51.70 90, 99.80, 90	106.04, 89.68, 50.99 90, 98.00, 90
Unique reflections^*	13229 (1747)	21275 (1021)
Overall redundancy^*	3.8 (3.9)	4.7 (3.2)
Completeness^* (%)	98.6 (98.5)	99.6 (93.9)
R_merge^* (%)	5.1 (117.6)	8.0 (83.2)
R_p.i.m. (I)^* (%)	4.7 (106.7)	4.0 (52.0)
⟨I/σ(I)⟩^*	11.9 (1.0)	9.0 (1.1)
CC(1/2)^* (%)	99.9 (58.4)	99.7 (74.1)
Refinement
PDB code	6FUZ	6FV0
R_factor (%)	23.3	20.8
R_free (%)	25.6	24.5
# non-H atoms protein water heterogen	3001 13 6 (GOL)	3039 90 7 (PEG)
Average B value (Å²)	113.04	65.81
rms bond lengths (Å)	0.009	0.007
rms bond angles (°)	1.08	0.93

*Numbers in parentheses refer to the highest resolution bin.

elife-38770-v2.xml

10.7554/eLife.38770.014

Table 3.X-ray Data collection and refinement statistics

	EC11-EL
Data collection
Wavelength (Å)	0.98
Resolution range (Å)	54.23–1.40 (1.45–1.40)
Space group	P 43 21 2
Unit cell
a, b, c (Å)	57.68, 57.68, 159.18
Α, β, γ (°)	90, 90, 90
Total reflections	522785 (35483)
Unique reflections	53914 (5195)
Multiplicity	9.7 (6.8)
Completeness (%)	99.73 (98.04)
Mean I/sigma(I)	25.05 (2.32)
Wilson B-factor	24.1
R-merge	0.036 (0.52)
R-meas	0.037 (0.57)
R-pim	0.011 (0.21)
CC1/2 (%)	100 (30.7)
CC* (%)	100 (68.5)
Refinement
Reflections used in refinement	53914 (5195)
Reflections used for R-free	2696 (260)
R-work (%)	16.9 (33.3)
R-free (%)	19.5 (34.7)
CC(work) (%)	96.5 (57.5)
CC(free) (%)	95.7 (65.0)
Number of non-hydrogen atoms	2141
macromolecules	1938
ligands	11
solvent	192
Protein residues	244
RMS(bonds)	0.006
RMS(angles)	0.75
Ramachandran favored (%)	98.76
Ramachandran allowed (%)	1.24
Ramachandran outliers (%)	0
Rotamer outliers (%)	0
Clashscore	2.55
Average B-factor	39.62
macromolecules	39
ligands	68.95
solvent	44.16

*Values in parentheses are for highest-resolution shell.

elife-38770-v3.xml

10.7554/eLife.38770.014

Table 3.X-ray Data collection and refinement statistics

	EC11-EL
Data collection
Wavelength (Å)	0.98
Resolution range (Å)	54.23–1.40 (1.45–1.40)
Space group	P 43 21 2
Unit cell
a, b, c (Å)	57.68, 57.68, 159.18
Α, β, γ (°)	90, 90, 90
Total reflections	522785 (35483)
Unique reflections	53914 (5195)
Multiplicity	9.7 (6.8)
Completeness (%)	99.73 (98.04)
Mean I/sigma(I)	25.05 (2.32)
Wilson B-factor	24.1
R-merge	0.036 (0.52)
R-meas	0.037 (0.57)
R-pim	0.011 (0.21)
CC1/2 (%)	100 (30.7)
CC* (%)	100 (68.5)
Refinement
Reflections used in refinement	53914 (5195)
Reflections used for R-free	2696 (260)
R-work (%)	16.9 (33.3)
R-free (%)	19.5 (34.7)
CC(work) (%)	96.5 (57.5)
CC(free) (%)	95.7 (65.0)
Number of non-hydrogen atoms	2141
macromolecules	1938
ligands	11
solvent	192
Protein residues	244
RMS(bonds)	0.006
RMS(angles)	0.75
Ramachandran favored (%)	98.76
Ramachandran allowed (%)	1.24
Ramachandran outliers (%)	0
Rotamer outliers (%)	0
Clashscore	2.55
Average B-factor	39.62
macromolecules	39
ligands	68.95
solvent	44.16

*Values in parentheses are for highest-resolution shell.

elife-48968-v2.xml

10.7554/eLife.48968.008

Table 1.X-ray data collection and refinement statistics.

Resolution range	39.7–2.1 (2.174–2.1)
Space group	P 1
Unit cell dimensions a, b, c (Å) α, β, γ (°)	42.75, 74.38, 81.55 107.17, 104.40, 101.76
Total reflections^*	180,242 (13587)
Unique reflections	26,619 (4934)
Multiplicity	6.8 (7.0)
Completeness (%)	96.6 (95.3)
Mean I/sigma(I)	11.8 (2.5)
Wilson B-factor	41.2
R-merge	0.101 (0.795)
R-meas	0.109 (0.858)
R-pim	0.041 (0.322)
CC_1/2	0.995 (0.885)
Refinement
Reflections used in refinement	50,102 (4931)
Reflections used for R-free	2000 (197)
R-work	0.198 (0.296)
R-free	0.240 (0.343)
Number of atoms
protein	6565
RNA	266
Solvent	189
RMSD bonds (Å)	0.003
RMSD angles (°)	0.82
Ramachandran favored (%)	98.38
Ramachandran allowed (%)	1.62
Ramachandran outliers (%)	0.00
Average B-factors (Å²)
protein	53.6
RNA	76.7
solvent	52.2

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

elife-48968-v3.xml

10.7554/eLife.48968.008

Table 1.X-ray data collection and refinement statistics.

Resolution range	39.7–2.1 (2.174–2.1)
Space group	P 1
Unit cell dimensions a, b, c (Å) α, β, γ (°)	42.75, 74.38, 81.55 107.17, 104.40, 101.76
Total reflections^*	180,242 (13587)
Unique reflections	26,619 (4934)
Multiplicity	6.8 (7.0)
Completeness (%)	96.6 (95.3)
Mean I/sigma(I)	11.8 (2.5)
Wilson B-factor	41.2
R-merge	0.101 (0.795)
R-meas	0.109 (0.858)
R-pim	0.041 (0.322)
CC_1/2	0.995 (0.885)
Refinement
Reflections used in refinement	50,102 (4931)
Reflections used for R-free	2000 (197)
R-work	0.198 (0.296)
R-free	0.240 (0.343)
Number of atoms
protein	6565
RNA	266
Solvent	189
RMSD bonds (Å)	0.003
RMSD angles (°)	0.82
Ramachandran favored (%)	98.38
Ramachandran allowed (%)	1.62
Ramachandran outliers (%)	0.00
Average B-factors (Å²)
protein	53.6
RNA	76.7
solvent	52.2

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

elife-51913-v2.xml

Table 2.X-ray data collection and refinement statistics.

	EcoDMT-Br-BIT complex
Data collection
Space group	C2
Cell dimensions
a, b, c (Å)	150.0, 81.7, 95.6
α, β, γ (°)	90, 107.4, 90
Wavelength (Å)	0.92
Resolution (Å)	50–3.8 (3.9–3.8)^*
R_merge (%)	9.8 (154.6)
CC_½ (%)	100.0 (81.7)
I /σI	15.6 (2.1)
Completeness (%)	99.3 (99.3)
Redundancy	14.3 (13.9)
Refinement
Resolution (Å)	12–3.8
No. Reflections	10576
R_work/R_free (%)	21.6/25.8
No. atoms
Protein	3780
Ligand/ion	17
Water	-
B factors
Protein	171.3
Ligand/ion	237.1
r.m.s. deviations
Bond lengths (Å)	0.005
Bond angles (°)	0.65

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

elife-57081-v2.xml

Table 1.X-ray data collection and refinement statistics.

Parentheses indicate highest shell.

Data Collection	Phasing data set	Refinement data set
Wavelength (Å)	1.55	1.55
Space group	P4₃2₁2	P4₃2₁2
a, b, c (Å)	205.13, 205.13, 68.27	205.34, 205.34, 68.31
α, β, γ (°)	90, 90, 90	90, 90, 90
Resolution (Å)	41–2.7 (2.8–2.7)	29.3–2.9 (3.06–2.9)
R_merge	0.291 (1.736)	0.157 (2.22)
R_pim	0.049 (0.545)	0.064 (0.881)
I/σI	13.5 (0.8)	10.2 (1.2)
Completeness (%)	98.5 (85.3)	99.6 (100)
Redundancy	32.2 (9.1)	6.9 (7.0)
CC_1/2%	0.996 (0.303)	0.996 (0.505)
Refinement
Resolution (Å)	29.3–2.9
No. of Reflections:	61477
R_work	0.23
R_free	0.30
No. of atoms	7169
Protein	7040
Ligand	129
B-factors (Å²)
Protein	79.3
Ligands
R.M.S. deviations:	57
Bond lengths, rmsd (Å)	0.01
Bond angles, rmsd (°)	1.41
Ramachandran plot
Ramachandran favored (%)	86
Ramachandran allowed (%)	13
Ramachandran outliers (%)	0.5

elife-57887-v2.xml

Table 1.X-ray data collection and refinement statistics.

	EMC2•EMC9	EMC2•EMC9
	(S-SAD phasing)	(Molecular replacement)
Data collection
X-ray source	Diamond I23	Diamond I03
X-ray wavelength (Å)	2.7552	0.9763
Space group	P2₁2₁2₁	P2₁2₁2₁
Unit cell parameters
a, b, c (Å)	53.2 82.8 124.0	52.6 84.9 122.6
α, β, γ (°)	90.0 90.0 90.0	90.0 90.0 90.0
Resolution range (Å)	49.6–2.65 (2.78–2.65)	49.7–2.20 (2.27–2.2)
No. of reflections
Total	668148 (73113)	1486886 (128644)
Unique	16468 (2109)	28668 (2433)
Completeness (%)	99.7 (98.9)	100.0 (100.0)
Multiplicity	40.6 (34.7)	51.9 (52.9)
I/σ(I)	36.8 (1.8)	17.6 (1.9)
R_meas (%)	6.4 (214.6)	17.2 (465.7)
R_merge (%)	6.3 (211.5)	17.0 (461.3)
R_pim (%)	1.0 (35.3)	2.4 (63.7)
CC_1/2 (%)	100.0 (81.7)	100.0 (92.6)
Refinement
R_work/R_free (%)	-	20.3/25.0
RMS deviations
Bond length (Å)	-	0.007
Bond angle (°)	-	0.848
No. of atoms
Protein	-	3454
Ligands	-	72
Water	-	80
Average B-factors (Å²)
Total	-	70.6
Protein	-	71.7
Ligands and waters	-	65.4
Ramachandran (%)
Favored	-	96.4
Outliers	-	0.0
PDB Code:	-	6Y4L

^*(*) Values in brackets are for the highest resolution bin.