7M2P

Structure of the SARS-CoV-2 3CL protease in complex with inhibitor 18


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Y2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 M Ammonium phosphate dibasic, 17% w/v PEG3350, pH8.0.
Crystal Properties
Matthews coefficientSolvent content
2.7154.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.2α = 90
b = 80.74β = 97.12
c = 85.759γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 180 mm plate2020-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU R-AXIS IV1.54180

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.748.2599.90.99610.26.440302
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)
11.71.730.475

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 REPLACEMENTTHROUGHOUT6Y2E1.748.251.3440267198699.810.18670.18570.205841.8795
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms40

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
pointlessdata scaling
PHENIXdata processing