6WEN | pdb_00006wen

Crystal Structure of ADP ribose phosphatase of NSP3 from SARS-CoV-2 in the apo form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	289	34.3% PEG 5000 MME, 150 mM AMPD/Tris, pH 9.0, 30 mM K/NA tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.671	α = 90
b = 29.677	β = 103.52
c = 37.886	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS3 X 6M	mirrors	2020-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	1.35	50	95.7	0.089	0.994	24.13	6.2		32168		-3

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	1.35	1.37	91.4		0.483	0.747	2.65	2.7

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	6WCF	1.35	36.86	30573	1595	95.63	0.1057	0.1036	0.1	0.1441	0.14	RANDOM	13.639

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]
0.75		0.67	-0.19		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.408
r_dihedral_angle_4_deg	26.327
r_dihedral_angle_3_deg	9.359
r_dihedral_angle_1_deg	6.509
r_rigid_bond_restr	1.984
r_angle_refined_deg	1.659
r_angle_other_deg	1.592
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.408
r_dihedral_angle_4_deg	26.327
r_dihedral_angle_3_deg	9.359
r_dihedral_angle_1_deg	6.509
r_rigid_bond_restr	1.984
r_angle_refined_deg	1.659
r_angle_other_deg	1.592
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1273
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.