5RGP

PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102628 (Mpro-x0771)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.1515% PEG 4K, 5% DMSO, 0.1M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.9135.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.84α = 90
b = 53β = 103
c = 44.34γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-03-04SINGLE 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
12.0754.9799.50.130.1560.0850.9916.63.315618
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)
12.072.1295.70.7660.9270.5150.58531114

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 SYNTHESISTHROUGHOUT6LU72.0754.971482879099.40.1630.1610.2019RANDOM31.048
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]
1.5-0.37-0.07-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.489
r_dihedral_angle_4_deg15.366
r_dihedral_angle_3_deg14.37
r_dihedral_angle_1_deg8.019
r_mcangle_it3.356
r_mcbond_other2.241
r_mcbond_it2.23
r_angle_refined_deg1.511
r_angle_other_deg1.388
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.489
r_dihedral_angle_4_deg15.366
r_dihedral_angle_3_deg14.37
r_dihedral_angle_1_deg8.019
r_mcangle_it3.356
r_mcbond_other2.241
r_mcbond_it2.23
r_angle_refined_deg1.511
r_angle_other_deg1.388
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2347
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing