8G62 | pdb_00008g62

Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.1 M Bis_tris propane, pH 7.0, 2.8 M sodium acetate, 0.1 M glycine, 4 mM ligand
Crystal Properties
Matthews coefficientSolvent content
3.2762.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.02α = 90
b = 170.02β = 90
c = 97.588γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2021-01-29MSINGLE 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)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
12.1749.061000.14317.112.775825
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)
12.172.211001.9790.5071.2711.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1749.0671961379399.930.181340.179620.180.214450.21RANDOM55.623
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]
-0.08-0.080.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.836
r_dihedral_angle_4_deg17.673
r_dihedral_angle_3_deg15.231
r_dihedral_angle_1_deg6.267
r_long_range_B_refined6.116
r_long_range_B_other6.105
r_scangle_other4.196
r_mcangle_it2.878
r_mcangle_other2.878
r_scbond_it2.648
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.836
r_dihedral_angle_4_deg17.673
r_dihedral_angle_3_deg15.231
r_dihedral_angle_1_deg6.267
r_long_range_B_refined6.116
r_long_range_B_other6.105
r_scangle_other4.196
r_mcangle_it2.878
r_mcangle_other2.878
r_scbond_it2.648
r_scbond_other2.648
r_mcbond_it1.957
r_mcbond_other1.955
r_angle_refined_deg1.61
r_angle_other_deg1.274
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7463
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms227

Software

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