5RE7

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z30932204


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
1.9135.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.118α = 90
b = 52.802β = 103.13
c = 44.506γ = 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
11.7955.1999.40.1260.1480.0770.9946.13.624146
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)
11.791.8395.71.3771.6510.8930.3563.21370

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 SYNTHESISTHROUGHOUT6LU71.7955.0822929120499.50.17020.16730.225RANDOM27.429
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]
1.33-0.19-0.04-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg14.476
r_dihedral_angle_3_deg14.349
r_dihedral_angle_1_deg7.223
r_mcangle_it2.539
r_mcbond_it1.57
r_mcbond_other1.568
r_angle_refined_deg1.443
r_angle_other_deg1.338
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg14.476
r_dihedral_angle_3_deg14.349
r_dihedral_angle_1_deg7.223
r_mcangle_it2.539
r_mcbond_it1.57
r_mcbond_other1.568
r_angle_refined_deg1.443
r_angle_other_deg1.338
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing