cryo-em data collection and model statistics (5)

elife-47650-v2.xml

10.7554/eLife.47650.020

Table 1.Cryo-EM data collection and model statistics.

	GDF15/GFRAL /RET	GDNF/GFRα1/RET	NRTN/GFRα2/RET	ARTN/GFRα3/RET
Data collection and processing
Magnification	46,730	46,730	46,730	46,730
Voltage (kV)	300	300	300	300
Electron exposure (e^-/Å²)	50	50	50	50
Defocus range (µm)	1.6–3	1.6–3	1.6–3	1.6–3
Pixel size (Å)	1.07	1.07	1.07	1.07
Final particle number	520,480	37,098	247,157	114,344
Map resolution (Å)	3.7	4.4	3.4	3.5
Map Sharpening B factor	−190	−200	−140	−140
Model Refinement Rms deviations Bonds (Å) Angles (°) Validation Molprobity score Clashscore Rotamer outliers (%) Ramachandran plot Favored (%) Allowed (%) Outliers (%)	0.006 0.978 1.59 4.43 0.12 94.6 5.3 0.1	0.005 0.994 2.02 8.53 0.41 89.5 10.4 0.1	0.005 0.797 1.45 2.74 0 94.2 5.8 0	0.007 1.040 1.73 4.35 0.12 91.1 8.9 0

10.7554/eLife.48630.008

Table 1.Cryo-EM data collection and model statistics.

	IR-insulin complex
Data collection and processing
Magnification	46,730
Voltage (kV)	300
Electron exposure (e^-/Å²)	50
Defocus range (µm)	1.5 – 3
Pixel size (Å)	1.07
Final particle number	235,707
Map resolution (Å)	3.1
Map Sharpening B factor	−100
Model Refinement
Rms deviations
Bonds (Å)	0.007
Angels (°)	0.885
Validation
MolProbity score	1.66
Clashscore	3.36
Rotamer outliers (%)	0
Ramachandran plot
Favored (%)	90.52
Allowed (%)	9.33
Outliers (%)	0.15

10.7554/eLife.48630.008

Table 1.Cryo-EM data collection and model statistics.

	IR-insulin complex
Data collection and processing
Magnification	46,730
Voltage (kV)	300
Electron exposure (e^-/Å²)	50
Defocus range (µm)	1.5 – 3
Pixel size (Å)	1.07
Final particle number	235,707
Map resolution (Å)	3.1
Map Sharpening B factor	−100
Model Refinement
Rms deviations
Bonds (Å)	0.007
Angels (°)	0.885
Validation
MolProbity score	1.66
Clashscore	3.36
Rotamer outliers (%)	0
Ramachandran plot
Favored (%)	90.52
Allowed (%)	9.33
Outliers (%)	0.15

10.7554/eLife.48792.013

Table 1.Cryo-EM data collection and model statistics.

	TRPV2_{APO_1} (EMD-20677, PDB 6U84)	TRPV2_{APO_2} (EMD-20678, PDB 6U85)	TRPV2_{CBD_1} (EMD-20686, PDB 6U8A)	TRPV2_{CBD_2} (EMB-20682, PDB 6U88)
Data collection and processing
Magnification	81,000x		81,000x
Detector mode	super-resolution		counting
Voltage (kV)	300		300
Defocus range (μm)	0.8–3.0		0.8–3.0
Pixel size (Å)	1.06		1.06
Total extracted particles (no.)	1,181,347		2,290,820
Refined particles (no.)	598,859		710,728
Final particles (no.)	42,407	14,332	23,944	36,153
Symmetry imposed	C4	C4	C4	C4
Map sharpening B factor (Å²)	−82	−88	−51	−38
Map resolution (Å) FSC threshold	3.7 0.143	4.0 0.143	3.4 0.143	3.2 0.143
Model Refinement
Model resolution cut-off (Å)	3.7	4.0	3.4	3.2
Model composition Nonhydrogen atoms Protein residues Ligands	20,460 2520 0	20,140 2472 0	20,036 2468 CBD: 4	20,016 2444 CBD: 4
R.M.S. deviations Bond lengths (Å) Bond angles (°)	0.011 0.742	0.007 0.664	0.008 0.947	0.009 1.060
Validation MolProbity score Clashscore Poor rotamers (%) CαBLAM outliers (%) EMRinger score	1.69 5.36 0.90 1.14 1.72	2.06 11.75 0.18 0.84 3.03	1.37 3.39 0.37 0.50 2.61	1.38 4.23 0.55 2.18 2.55
Ramachandran plot Favored (%) Allowed (%) Disallowed (%)	93.97 6.03 0.00	92.31 7.69 0.00	96.38 3.62 0.00	96.97 3.03 0.00

10.7554/eLife.49572.019

Table 1.Cryo-EM data collection and model statistics

	ZINC9155420-Bound TRPV5 in nanodiscs (PDB: 6PBF, EMB-20292)	ZINC17988990-bound TRPV5 in nanodiscs (PDB: 6PBE, EMB-20291)
Data collection and processing
Magnification	~45,500	~45,500
Voltage (kV)	300	300
Defocus range (μm)	1.0–2.5	0.8–2.5
Pixel size (Å)	1.064	1.064
Symmetry imposed	C4	C4
Initial particle images (no.)	510,500	670,057
Final particle images (no.)	21,802	98,516
Map resolution (Å) FSC threshold	4.2 0.143	3.78 0.143
Map resolution range (Å)	3.5–5.5	3.0–5.0
Refinement
Model resolution cut-off (Å) FSC threshold	4.3 0.143	3.78 0.143
Map sharpening B factor (Å²)	−330	−253
Model composition	0	0
Nonhydrogen atoms	2392	2416
Protein residues	4	4
Ligands
R.m.s. deviations	0.005	0.006
Bond lengths (Å)	0.897	0.935
Bond angles (°)
Validation	1.70	1.72
MolProbity score	5.02	3.88
Clashscore	0.22	1.18
Poor rotamers (%)
Ramachandran plot	93.20	91.83
Favored (%)	6.80	8.17
Allowed (%)	0.00	0.00
Disallowed (%)