5RF3

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1741970824


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.1515% PEG 4K, 5% DMSO, 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
1.935.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.469α = 90
b = 52.697β = 103.06
c = 44.537γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-03-05SINGLE 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
11.554.7398.60.0980.1160.0620.9976.23.240199
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)
11.51.5293.91.3721.7121.010.3432.31883

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 SYNTHESISTHROUGHOUT6LU71.554.7838080194398.20.1870.18530.221RANDOM21.352
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]
1.44-0.9-0.13-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.143
r_dihedral_angle_4_deg16.625
r_dihedral_angle_3_deg13.266
r_dihedral_angle_1_deg6.956
r_mcangle_it2.171
r_angle_refined_deg1.472
r_angle_other_deg1.449
r_mcbond_other1.215
r_mcbond_it1.129
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.143
r_dihedral_angle_4_deg16.625
r_dihedral_angle_3_deg13.266
r_dihedral_angle_1_deg6.956
r_mcangle_it2.171
r_angle_refined_deg1.472
r_angle_other_deg1.449
r_mcbond_other1.215
r_mcbond_it1.129
r_chiral_restr0.073
r_bond_refined_d0.009
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 Atoms335
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing