5R82

PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z219104216


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1515% PEG 4K, 5% DMSO
Crystal Properties
Matthew coefficientSolvent content
1.9135.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.665α = 90
b = 52.848β = 102.97
c = 44.468γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-02-26SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9126DiamondI04-1

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
11.3154.9388.70.050.060.0320.9989.72.954169
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)
11.311.3343.81.0051.3780.9380.3781.41317

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6LU71.3154.950988260587.510.18190.18030.2116RANDOM18.397
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]
0.85-0.46-0.13-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.472
r_dihedral_angle_4_deg15.036
r_dihedral_angle_3_deg12.864
r_dihedral_angle_1_deg7.287
r_mcangle_it1.732
r_angle_refined_deg1.463
r_angle_other_deg1.405
r_mcbond_other0.979
r_mcbond_it0.907
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.472
r_dihedral_angle_4_deg15.036
r_dihedral_angle_3_deg12.864
r_dihedral_angle_1_deg7.287
r_mcangle_it1.732
r_angle_refined_deg1.463
r_angle_other_deg1.405
r_mcbond_other0.979
r_mcbond_it0.907
r_chiral_restr0.072
r_gen_planes_refined0.008
r_bond_refined_d0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing