7LB7

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


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.628718% PEG3350, 0.1 M Bis-Tris pH 6.6
Crystal Properties
Matthews coefficientSolvent content
2.1843.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.558α = 90
b = 55.691β = 101.31
c = 48.808γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 4M2020-10-20MSINGLE WAVELENGTH
21neutron293AREA DETECTORORNL ANGER CAMERA2020-10-15LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418
2SPALLATION SOURCEORNL Spallation Neutron Source BEAMLINE MANDI2.0 - 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
1254.2196.30.08213.94.219852
22.414.2983.40.17611.44.059566
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)
122.050.5441.94
22.42.490.3363.12.68

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 REPLACEMENT2402.51926198497.50.2040.225RANDOM38.51
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.414.922.5953947082.80.2160.228RANDOM
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
o_angle_deg1.1
o_bond_d0.009
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
RMS Deviations
KeyRefinement Restraint Deviation
o_angle_deg1.1
o_bond_d0.009
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2368
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms49

Software

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