6WEN

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)
TypeSourceAccession CodeDetails
experimental modelPDB 6WCF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP928934.3% PEG 5000 MME, 150 mM AMPD/Tris, pH 9.0, 30 mM K/NA tartrate
Crystal Properties
Matthews coefficientSolvent content
2.1141.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.671α = 90
b = 29.677β = 103.52
c = 37.886γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6Mmirrors2020-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.355095.70.0890.99424.136.232168-3
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)RedundancyNumber Unique Reflections (All)
11.351.3791.40.4830.7472.652.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6WCF1.3536.8630573159595.630.10570.10360.1441RANDOM13.639
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]
0.750.67-0.19-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.408
r_dihedral_angle_4_deg26.327
r_dihedral_angle_3_deg9.359
r_dihedral_angle_1_deg6.509
r_rigid_bond_restr1.984
r_angle_refined_deg1.659
r_angle_other_deg1.592
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.408
r_dihedral_angle_4_deg26.327
r_dihedral_angle_3_deg9.359
r_dihedral_angle_1_deg6.509
r_rigid_bond_restr1.984
r_angle_refined_deg1.659
r_angle_other_deg1.592
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1273
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing