7ORW | pdb_00007orw

Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00265

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZPE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293	Protein - 63 mg/mL in 50 mM Tris/HCl pH 8.0, 150 mM NaCl; precipitant (reservoir) - 0.1 M Bis-Tris/HCl pH 6.7, 2.4 M NaCl; 1:1, 1:2, 2:1 protein-to-precipitant ratios, 300 nL total drop volume. Soaking: reservoir solution, supplemented to 50 mM ligand, 5% (v/v) DMSO, 15% (v/v) glycerol; 2 h, 293K.

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.771	α = 90
b = 107.771	β = 90
c = 107.771	γ = 90

Symmetry
Space Group	I 21 3

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 EIGER X 16M		2020-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9788	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	76.21	100	0.075	0.08	0.028	0.998	13.5	8.4		15364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	100		1.325	1.42	0.506	0.567		7.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6ZPE	1.95	53.94	14605	759	99.98	0.1761	0.1745	0.18	0.2086	0.22	RANDOM	48.539

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.839
r_dihedral_angle_3_deg	12.475
r_dihedral_angle_1_deg	6.402
r_dihedral_angle_4_deg	2.814
r_angle_other_deg	1.327
r_angle_refined_deg	1.313
r_chiral_restr	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.839
r_dihedral_angle_3_deg	12.475
r_dihedral_angle_1_deg	6.402
r_dihedral_angle_4_deg	2.814
r_angle_other_deg	1.327
r_angle_refined_deg	1.313
r_chiral_restr	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	909
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.