5ESB

Crystal structure of a genotype 1a/3a chimeric HCV NS3/4A protease in complex with Vaniprevir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M5M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298100mM MES buffer pH 6.5, 4% (w/v) ammonium sulfate, 20-26% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.119α = 90
b = 58.403β = 90
c = 60.016γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5

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
12.433.394.10.06219.54.57436
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)
12.42.46970.1394.4

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 REPLACEMENTTHROUGHOUT3m5m2.433655974491.180.18710.18190.2329RANDOM21.417
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]
0.35-0.03-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_3_deg14.449
r_dihedral_angle_4_deg12.596
r_dihedral_angle_1_deg6.557
r_angle_refined_deg1.606
r_mcangle_it1.455
r_angle_other_deg1.277
r_mcbond_it0.817
r_mcbond_other0.809
r_chiral_restr0.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.342
r_dihedral_angle_3_deg14.449
r_dihedral_angle_4_deg12.596
r_dihedral_angle_1_deg6.557
r_angle_refined_deg1.606
r_mcangle_it1.455
r_angle_other_deg1.277
r_mcbond_it0.817
r_mcbond_other0.809
r_chiral_restr0.289
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1380
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms64

Software

Software
Software NamePurpose
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction