7N8C

Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule5948770040


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729318% PEG3350, 0.1 M Bis-Tris pH 7.0 reservoir solution and 0.2 microL microseeds at 1:200 dilution
Crystal Properties
Matthews coefficientSolvent content
2.9357.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.314α = 90
b = 81.301β = 96.46
c = 88.578γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4MOSMIC VARIMAX2021-03-10MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERACOLLIMATORS2021-03-03LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54
2SPALLATION SOURCEORNL Spallation Neutron Source BEAMLINE MANDI2.00-4.16ORNL 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
12.259.7296.30.1070.0550.99211.44.719108
22.512.8685.60.2120.0960.94615.65.511534
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)
12.22.270.6020.6861.64.8
22.52.590.2835.85.6

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 REPLACEMENT2.225.92.51747685688.10.1770.192RANDOM44.13
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.512.862.51153257784.90.1870.211RANDOM44.13
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_deg27.1
x_torsion_deg27.1
x_angle_deg1.1
x_angle_deg1.1
x_torsion_impr_deg0.86
x_torsion_impr_deg0.86
x_bond_d0.008
x_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms24

Software

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