5RF1

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00023830


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
1.935.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.485α = 90
b = 52.653β = 102.74
c = 44.429γ = 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
11.7354.8399.50.130.1540.080.9955.73.526473
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)
11.731.7696.91.7022.0561.1340.32731416

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 SYNTHESISTHROUGHOUT6LU71.7354.8625096131499.260.18870.18620.2361RANDOM25.89
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]
1.82-1.43-0.31-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.506
r_dihedral_angle_3_deg14.361
r_dihedral_angle_4_deg13.574
r_dihedral_angle_1_deg7.985
r_mcangle_it2.636
r_mcbond_other1.665
r_mcbond_it1.662
r_angle_refined_deg1.457
r_angle_other_deg1.339
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.506
r_dihedral_angle_3_deg14.361
r_dihedral_angle_4_deg13.574
r_dihedral_angle_1_deg7.985
r_mcangle_it2.636
r_mcbond_other1.665
r_mcbond_it1.662
r_angle_refined_deg1.457
r_angle_other_deg1.339
r_chiral_restr0.067
r_bond_refined_d0.008
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 Atoms334
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing