5RG1

PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00024905


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
1.9135.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.585α = 90
b = 52.61β = 103.09
c = 44.852γ = 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
11.6554.8499.70.1430.1680.0870.9915.13.530785
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)
11.651.6898.81.4631.7770.9940.3342.91519

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 SYNTHESISTHROUGHOUT6LU71.6554.8329207151999.450.17410.17190.2152RANDOM20.451
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]
1.13-0.53-0.11-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.701
r_dihedral_angle_1_deg19.671
r_dihedral_angle_4_deg15.225
r_dihedral_angle_3_deg13.919
r_mcangle_it2.277
r_angle_refined_deg1.541
r_mcbond_other1.475
r_mcbond_it1.465
r_angle_other_deg1.441
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.701
r_dihedral_angle_1_deg19.671
r_dihedral_angle_4_deg15.225
r_dihedral_angle_3_deg13.919
r_mcangle_it2.277
r_angle_refined_deg1.541
r_mcbond_other1.475
r_mcbond_it1.465
r_angle_other_deg1.441
r_chiral_restr0.077
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 Atoms332
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing