7SGV

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6WRH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72773 M sodium chloride, 0.1 M Bis_tris buffer, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
3.7166.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.982α = 90
b = 82.982β = 90
c = 134.021γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1244.71990.1890.2010.0650.97778.836245
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)RedundancyNumber Unique Reflections (All)
122.0379.41.2541.3570.5030.4971.016.1

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 REPLACEMENTTHROUGHOUT6WRH244.7134398180599.020.18190.18060.2074RANDOM58.973
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]
0.560.280.56-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.05
r_dihedral_angle_4_deg26.61
r_dihedral_angle_3_deg14.964
r_dihedral_angle_1_deg6.281
r_angle_refined_deg1.486
r_angle_other_deg1.367
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.05
r_dihedral_angle_4_deg26.61
r_dihedral_angle_3_deg14.964
r_dihedral_angle_1_deg6.281
r_angle_refined_deg1.486
r_angle_other_deg1.367
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.008
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2452
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms24

Software

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