5RFH

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102277


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
1.935.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.297α = 90
b = 52.885β = 103.11
c = 44.537γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-03-06SINGLE 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
11.5854.7898.40.1060.1270.0680.9955.13.234396
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)
11.581.6195.51.4041.7531.0310.2942.41708

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 SYNTHESISTHROUGHOUT6LU71.5854.6932141167396.620.1910.18860.2368RANDOM22.267
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]
0.84-0.340.32-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.64
r_dihedral_angle_4_deg19.245
r_dihedral_angle_3_deg13.893
r_dihedral_angle_1_deg8.589
r_mcangle_it2.228
r_angle_refined_deg1.5
r_angle_other_deg1.387
r_mcbond_other1.375
r_mcbond_it1.368
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.64
r_dihedral_angle_4_deg19.245
r_dihedral_angle_3_deg13.893
r_dihedral_angle_1_deg8.589
r_mcangle_it2.228
r_angle_refined_deg1.5
r_angle_other_deg1.387
r_mcbond_other1.375
r_mcbond_it1.368
r_chiral_restr0.072
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 Atoms330
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing