5R84

PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1515% PEG 4K, 5% DMSO
Crystal Properties
Matthew coefficientSolvent content
1.9336.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.146α = 90
b = 53.167β = 101.66
c = 44.267γ = 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
11.8355.499.70.140.1640.0840.9955.63.722904
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)
11.831.9399.81.6191.8780.9410.4553.83333

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 SYNTHESISTHROUGHOUT6LU71.8355.421632115299.040.22050.21670.2926RANDOM38.925
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]
1.572.78-2.47-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.627
r_dihedral_angle_3_deg14.761
r_dihedral_angle_4_deg13.273
r_dihedral_angle_1_deg7.892
r_mcangle_it3.562
r_mcbond_other2.154
r_mcbond_it1.899
r_angle_refined_deg1.412
r_angle_other_deg1.256
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.627
r_dihedral_angle_3_deg14.761
r_dihedral_angle_4_deg13.273
r_dihedral_angle_1_deg7.892
r_mcangle_it3.562
r_mcbond_other2.154
r_mcbond_it1.899
r_angle_refined_deg1.412
r_angle_other_deg1.256
r_chiral_restr0.062
r_gen_planes_refined0.006
r_bond_refined_d0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing