7NFV

Structure of SARS-CoV-2 Papain-like protease PLpro


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JRN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2771.0M NaH2PO4/1.0MKH2PO4 100mM Tris_HCl pH=7.5
Crystal Properties
Matthews coefficientSolvent content
3.6866

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.33α = 90
b = 82.33β = 90
c = 134.32γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4248.891000.9728.352.999793
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.440.36

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7jrn1.4248.8999791491999.9890.1550.15380.171431.543
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]
0.2990.150.299-0.972
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.599
r_dihedral_angle_3_deg14.271
r_dihedral_angle_4_deg12.021
r_lrange_it7.261
r_lrange_other6.907
r_dihedral_angle_1_deg6.089
r_scangle_it5.636
r_scangle_other5.631
r_scbond_it3.892
r_scbond_other3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.599
r_dihedral_angle_3_deg14.271
r_dihedral_angle_4_deg12.021
r_lrange_it7.261
r_lrange_other6.907
r_dihedral_angle_1_deg6.089
r_scangle_it5.636
r_scangle_other5.631
r_scbond_it3.892
r_scbond_other3.89
r_mcangle_it2.607
r_mcangle_other2.606
r_angle_refined_deg2.308
r_mcbond_it1.94
r_mcbond_other1.939
r_angle_other_deg1.609
r_symmetry_nbd_refined0.314
r_symmetry_xyhbond_nbd_refined0.266
r_xyhbond_nbd_refined0.245
r_nbd_refined0.244
r_nbd_other0.213
r_nbtor_refined0.187
r_symmetry_nbd_other0.18
r_chiral_restr0.119
r_symmetry_xyhbond_nbd_other0.091
r_symmetry_nbtor_other0.088
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2502
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing