7TDU

Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with BBH-1


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7N8C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.628720% PEG3350, 0.1 M Bis-Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9157.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.02α = 90
b = 81.217β = 96.72
c = 88.825γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4MOSMIC VARIMAX2021-10-11MSINGLE WAVELENGTH
21neutron293IMAGE PLATEMAATELCOLLIMATORS2021-10-05LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54
2NUCLEAR REACTORILL BEAMLINE LADI III3.0-4.0ILLLADI III

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.8559.7596.60.07613.65.432013
22.244.0478.70.1610.0940.9867.93.115471
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.920.6711.45.4
22.22.320.3670.2230.8252.12.9

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.8529.883314728704141586.60.1970.2133.86
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.229.9197601306065266.10.2370.25733.86
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
x_torsion_deg29.4
x_torsion_deg29.4
x_angle_deg1.2
x_angle_deg1.2
x_torsion_impr_deg0.88
x_torsion_impr_deg0.88
x_bond_d0.011
x_bond_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms45

Software

Software
Software NamePurpose
nCNSrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
nCNSphasing
LAUEGENdata reduction
LSCALEdata scaling