5SBF

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NendoU

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	0.1 M Na3 Citrate pH 5,14% w/v PEG6000

Crystal Properties
Matthews coefficient	Solvent content
4.62	73.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.997	α = 90
b = 149.997	β = 90
c = 111.405	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2020-01-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9127	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.64	130.31	99.9	0.09	1	12.2			1560712

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.67	98.7		2.458	0.33			8585

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6X1B	1.64	129.98	161483	8654	97.8	0.1887	0.1875	0.2111	RANDOM	32.016

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.74	-0.37		-0.74		2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.724
r_dihedral_angle_3_deg	13.715
r_dihedral_angle_4_deg	12.607
r_dihedral_angle_1_deg	7.173
r_mcangle_it	3.986
r_mcbond_it	2.886
r_mcbond_other	2.885
r_angle_refined_deg	1.767
r_angle_other_deg	1.5
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.724
r_dihedral_angle_3_deg	13.715
r_dihedral_angle_4_deg	12.607
r_dihedral_angle_1_deg	7.173
r_mcangle_it	3.986
r_mcbond_it	2.886
r_mcbond_other	2.885
r_angle_refined_deg	1.767
r_angle_other_deg	1.5
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5498
Nucleic Acid Atoms
Solvent Atoms	966
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.