7JUN

Joint neutron/X-ray structure of SARS-CoV-2 3CL Mpro at room temperature


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28718% PEG3350, 0.1 M Bis-Tris pH 6.6, 3% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.0640.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.927α = 90
b = 54.686β = 101.46
c = 45.216γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4M2020-07-20MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERA2020-07-15LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54
2SPALLATION SOURCEORNL Spallation Neutron Source BEAMLINE MANDI2.0-4.0ORNL Spallation Neutron SourceMANDI

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
12.356.3297.90.1290.070.9919.314.312094
12.514.9583.90.19135.78031
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)
12.32.380.5890.3550.51.63.7
12.52.590.3333.74.7

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 REPLACEMENT2.328.161017953782.40.1850.2240.27
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.514.96801841383.50.2010.25340.27
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_deg17.7
x_torsion_deg17.7
x_angle_deg1.1
x_angle_deg1.1
x_torsion_impr_deg1
x_torsion_impr_deg1
x_bond_d0.008
x_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms

Software

Software
Software NamePurpose
nCNSrefinement
PHASERphasing
CrysalisProdata reduction
CrysalisProdata scaling
Mantiddata reduction
Mantiddata scaling