7LMJ

SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N-(4-(2-oxo-1,2-dihydropyridin-3-yl)phenyl)acetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VB3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.629510% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.3763.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.539α = 90
b = 82.712β = 105.299
c = 53.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX-3002020-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.978APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.68632.35699.50.02917.067.450084
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6861.750.2421

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE3VB31.68632.35650084250698.8470.1480.14560.191738.825
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]
-0.169-0.2390.531-0.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.351
r_dihedral_angle_4_deg16.714
r_dihedral_angle_3_deg14.495
r_scangle_it8.04
r_scangle_other8.038
r_scbond_it7.63
r_scbond_other7.627
r_dihedral_angle_1_deg7.368
r_lrange_it7.288
r_lrange_other7.143
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2371
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing