7NTV

Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (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 DN_EG_002 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.
Crystal Properties
Matthews coefficientSolvent content
2.6152.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.941α = 90
b = 99.743β = 90
c = 104.126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00003SLSX06SA

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
12.06549.42399.820.1580.1640.0440.9981113.544110
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)
12.0652.11998.91.9610.540.711.613.75

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 REPLACEMENTTHROUGHOUT6lu72.06549.42344049220399.8140.1960.19490.2275RANDOM42.474
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]
-1.7532.332-0.579
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg15.226
r_dihedral_angle_3_deg15.116
r_lrange_it8.672
r_lrange_other8.668
r_dihedral_angle_1_deg7.582
r_scangle_it6.911
r_scangle_other6.91
r_mcangle_it5.07
r_mcangle_other5.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg15.226
r_dihedral_angle_3_deg15.116
r_lrange_it8.672
r_lrange_other8.668
r_dihedral_angle_1_deg7.582
r_scangle_it6.911
r_scangle_other6.91
r_mcangle_it5.07
r_mcangle_other5.07
r_scbond_it4.57
r_scbond_other4.569
r_mcbond_other3.543
r_mcbond_it3.54
r_angle_refined_deg1.633
r_angle_other_deg1.369
r_nbd_other0.256
r_symmetry_nbd_refined0.224
r_nbd_refined0.2
r_symmetry_nbd_other0.192
r_symmetry_xyhbond_nbd_refined0.186
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.153
r_symmetry_nbtor_other0.08
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4687
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
Cootmodel building
PHASERphasing
pointlessdata scaling
XDSdata reduction