7Q5E

Crystal structure of F2F-2020209-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BB2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.12M 1,6-Hexanediol 0.12M 1-Butanol 0.12M 1,2-Propanediol 0.12M 2-Propanol 0.12M 1,4-Butanediol 0.12M 1,3-Propanediol, 0.1M Tris/bicine pH 8.5, 20% v/v PEG 500 MME 10 % w/v PEG 20000 0.1 M Buffer System 3 8.5 30 % v/v Precipitant Mix 1
Crystal Properties
Matthews coefficientSolvent content
2.6253.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.978α = 90
b = 101.017β = 90
c = 103.437γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.000ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.67101.021000.0720.99916.27.48330322.64
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.70.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7BB21.6746.041.3483196423199.950.17190.17070.193633.45
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.0006
f_angle_d1.0128
f_chiral_restr0.0609
f_bond_d0.0096
f_plane_restr0.0077
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4726
Nucleic Acid Atoms
Solvent Atoms591
Heterogen Atoms81

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing