5REC

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1587220559


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
1.935.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.398α = 90
b = 52.72β = 102.89
c = 44.4γ = 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
11.7354.8499.60.1210.1430.0750.9965.93.526494
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)
11.731.7697.51.4251.730.9650.3153.11468

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 SYNTHESISTHROUGHOUT6LU71.7354.7825121131499.420.18530.18260.2371RANDOM26.783
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]
2.2-1.3-0.74-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.872
r_dihedral_angle_3_deg14.163
r_dihedral_angle_4_deg11.798
r_dihedral_angle_1_deg7.736
r_mcangle_it2.779
r_mcbond_it1.785
r_mcbond_other1.785
r_angle_refined_deg1.456
r_angle_other_deg1.363
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.872
r_dihedral_angle_3_deg14.163
r_dihedral_angle_4_deg11.798
r_dihedral_angle_1_deg7.736
r_mcangle_it2.779
r_mcbond_it1.785
r_mcbond_other1.785
r_angle_refined_deg1.456
r_angle_other_deg1.363
r_chiral_restr0.066
r_bond_refined_d0.008
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 Atoms329
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing