7NUK

Crystal structure of SARS CoV2 main protease in complex with EG009 (modelled using PanDDA event map)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LU7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock EG009 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM EG009 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
Crystal Properties
Matthews coefficientSolvent content
2.643911453.506916

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.979α = 90
b = 100.929β = 90
c = 104.183γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00036SLSX06SA

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
12.1946.2999.30.2540.2640.0710.9979.613.537312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.192.2698.72.5870.7410.6991.413.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6lu72.1946.2937256186299.0880.2180.21550.2608RANDOM38.769
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]
-3.6035.503-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.9
r_dihedral_angle_3_deg16.7
r_dihedral_angle_4_deg16.283
r_dihedral_angle_1_deg7.796
r_lrange_it7.128
r_lrange_other7.125
r_scangle_it5.284
r_scangle_other5.284
r_mcangle_it4.26
r_mcangle_other4.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.9
r_dihedral_angle_3_deg16.7
r_dihedral_angle_4_deg16.283
r_dihedral_angle_1_deg7.796
r_lrange_it7.128
r_lrange_other7.125
r_scangle_it5.284
r_scangle_other5.284
r_mcangle_it4.26
r_mcangle_other4.26
r_scbond_it3.112
r_scbond_other3.111
r_mcbond_it2.558
r_mcbond_other2.554
r_angle_refined_deg1.54
r_angle_other_deg1.272
r_nbd_other0.214
r_symmetry_nbd_refined0.203
r_nbd_refined0.193
r_symmetry_xyhbond_nbd_refined0.193
r_symmetry_nbd_other0.183
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.16
r_symmetry_nbtor_other0.078
r_chiral_restr0.069
r_symmetry_xyhbond_nbd_other0.046
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4725
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building