5RE6

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z54571979


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
1.9135.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.56α = 90
b = 52.81β = 103.2
c = 44.62γ = 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
11.8747.5799.80.230.2690.1370.9844.33.821176
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)
11.871.921002.4392.8231.4050.3493.91561

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 SYNTHESISTHROUGHOUT6LU71.8747.6220092107799.730.18890.18570.2505RANDOM26.744
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]
1.42-1.370.05-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.19
r_dihedral_angle_4_deg18.83
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg7.935
r_mcangle_it2.882
r_mcbond_other1.917
r_mcbond_it1.915
r_angle_refined_deg1.575
r_angle_other_deg1.341
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.19
r_dihedral_angle_4_deg18.83
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg7.935
r_mcangle_it2.882
r_mcbond_other1.917
r_mcbond_it1.915
r_angle_refined_deg1.575
r_angle_other_deg1.341
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing