5REA

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z31432226


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.1515% PEG 4K, 5% DMSO, 0.1M MES
Crystal Properties
Matthew coefficientSolvent content
1.8734.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.604α = 90
b = 52.401β = 102.78
c = 44.322γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-02-27SINGLE 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
11.6354.4799.50.0960.1140.060.9966.23.431096
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)
11.631.6698.21.4341.7550.9960.362.81626

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 SYNTHESISTHROUGHOUT6LU71.6354.4229231151398.260.18740.18520.2282RANDOM27.719
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]
1.66-1.05-0.39-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.273
r_dihedral_angle_4_deg16.428
r_dihedral_angle_3_deg13.386
r_dihedral_angle_1_deg6.988
r_mcangle_it2.113
r_angle_refined_deg1.347
r_angle_other_deg1.281
r_mcbond_other1.013
r_mcbond_it0.94
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.273
r_dihedral_angle_4_deg16.428
r_dihedral_angle_3_deg13.386
r_dihedral_angle_1_deg6.988
r_mcangle_it2.113
r_angle_refined_deg1.347
r_angle_other_deg1.281
r_mcbond_other1.013
r_mcbond_it0.94
r_chiral_restr0.06
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing