2H9H

An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52972.5% PEG 8000, 1.5% Glycerol, 10mM tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.1542.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.672α = 90
b = 56.055β = 90
c = 80.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.3526.4981.20.05612.736919
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)
11.351.422.60.3072.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2A4O1.3926.493434234294183886.70.1820.1810.197RANDOM20.97
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]
1.22-0.55-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.315
r_dihedral_angle_4_deg20.304
r_dihedral_angle_3_deg11.773
r_dihedral_angle_1_deg6.008
r_scangle_it5.829
r_scbond_it3.98
r_mcangle_it2.905
r_mcbond_it1.899
r_angle_refined_deg1.2
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.315
r_dihedral_angle_4_deg20.304
r_dihedral_angle_3_deg11.773
r_dihedral_angle_1_deg6.008
r_scangle_it5.829
r_scbond_it3.98
r_mcangle_it2.905
r_mcbond_it1.899
r_angle_refined_deg1.2
r_nbtor_refined0.307
r_nbd_refined0.205
r_symmetry_vdw_refined0.142
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.1
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1667
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing