5REB

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899


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
1.9235.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.212α = 90
b = 53.034β = 102.95
c = 44.302γ = 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
11.6855.2299.50.0930.110.0580.9976.93.529211
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)
11.681.7195.71.1571.4290.8260.3282.91432

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 SYNTHESISTHROUGHOUT6LU71.6855.1727647143499.160.17790.17550.2237RANDOM26.546
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]
1.24-0.09-0.31-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.384
r_dihedral_angle_4_deg14.245
r_dihedral_angle_3_deg14.108
r_dihedral_angle_1_deg7.827
r_mcangle_it2.7
r_mcbond_other1.727
r_mcbond_it1.723
r_angle_refined_deg1.547
r_angle_other_deg1.414
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.384
r_dihedral_angle_4_deg14.245
r_dihedral_angle_3_deg14.108
r_dihedral_angle_1_deg7.827
r_mcangle_it2.7
r_mcbond_other1.727
r_mcbond_it1.723
r_angle_refined_deg1.547
r_angle_other_deg1.414
r_chiral_restr0.075
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 Atoms341
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing