2VJ1

A Structural View of the Inactivation of the SARS-Coronavirus Main Proteinase by Benzotriazole Esters


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UJ1PDB ENTRY 1UJ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.55% PEG10000, 0.1M MES PH6.5, 3% ETHYLNE GLYCOL, 50MM NH4-ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.550.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.231α = 90
b = 97.76β = 103.01
c = 67.709γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBENT MIRROR2005-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.2539.2799.70.0712.93.231422238.14
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)
12.252.341000.471.913.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1UJ12.2565.9429847157599.80.1870.1830.256RANDOM43.84
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]
1.521.280.84-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.732
r_dihedral_angle_4_deg20.608
r_dihedral_angle_3_deg18.444
r_dihedral_angle_1_deg7.518
r_scangle_it3.171
r_scbond_it2.173
r_angle_refined_deg1.574
r_mcangle_it1.481
r_mcbond_it0.867
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.732
r_dihedral_angle_4_deg20.608
r_dihedral_angle_3_deg18.444
r_dihedral_angle_1_deg7.518
r_scangle_it3.171
r_scbond_it2.173
r_angle_refined_deg1.574
r_mcangle_it1.481
r_mcbond_it0.867
r_nbtor_refined0.31
r_nbd_refined0.216
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.21
r_symmetry_hbond_refined0.159
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4652
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing