5R83

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z44592329


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1515% PEG 4K, 5% DMSO
Crystal Properties
Matthew coefficientSolvent content
1.8935.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.267α = 90
b = 52.583β = 102.95
c = 44.535γ = 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
11.5854.6599.60.10.1180.0610.9976.73.434692
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)
11.581.6197.31.4341.7711.0220.3352.61688

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 SYNTHESISTHROUGHOUT6LU71.5854.7132895171499.390.17780.17580.2149RANDOM21.487
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]
1.26-1.07-0.41-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.308
r_dihedral_angle_3_deg13.737
r_dihedral_angle_4_deg13.198
r_dihedral_angle_1_deg8.055
r_mcangle_it2.493
r_mcbond_other1.647
r_mcbond_it1.638
r_angle_refined_deg1.565
r_angle_other_deg1.453
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.308
r_dihedral_angle_3_deg13.737
r_dihedral_angle_4_deg13.198
r_dihedral_angle_1_deg8.055
r_mcangle_it2.493
r_mcbond_other1.647
r_mcbond_it1.638
r_angle_refined_deg1.565
r_angle_other_deg1.453
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms328
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing