5RFI

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102353


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
1.935.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.157α = 90
b = 52.936β = 103.03
c = 44.403γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-03-05SINGLE 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
11.6954.6698.50.1160.1390.0740.9955.33.328100
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)
11.691.7296.91.4121.7290.980.3792.91423

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 SYNTHESISTHROUGHOUT6LU71.6954.6426261135596.70.19570.19330.2423RANDOM25.921
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]
0.4-0.341.05-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.946
r_dihedral_angle_4_deg16.167
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg7.428
r_mcangle_it2.387
r_mcbond_other1.379
r_angle_refined_deg1.363
r_angle_other_deg1.31
r_mcbond_it1.284
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.946
r_dihedral_angle_4_deg16.167
r_dihedral_angle_3_deg13.657
r_dihedral_angle_1_deg7.428
r_mcangle_it2.387
r_mcbond_other1.379
r_angle_refined_deg1.363
r_angle_other_deg1.31
r_mcbond_it1.284
r_chiral_restr0.068
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing