7JIW

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62770.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder530
Crystal Properties
Matthews coefficientSolvent content
4.9575.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.648α = 90
b = 113.648β = 90
c = 220.574γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2020-06-29MSINGLE 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)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
12.345.5199.90.0950.0970.0216.320.93230866.3
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)
12.32.34991.7311.7880.4280.6050.9714.6

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 REPLACEMENTTHROUGHOUT6WZU2.345.5130715156499.850.21350.21210.2395RANDOM82.634
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]
2.872.87-5.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.544
r_dihedral_angle_3_deg15.408
r_dihedral_angle_4_deg14.762
r_dihedral_angle_1_deg6.843
r_angle_refined_deg1.489
r_angle_other_deg1.214
r_chiral_restr0.059
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.544
r_dihedral_angle_3_deg15.408
r_dihedral_angle_4_deg14.762
r_dihedral_angle_1_deg6.843
r_angle_refined_deg1.489
r_angle_other_deg1.214
r_chiral_restr0.059
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2422
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms47

Software

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