3SU0

Crystal structure of NS3/4A protease variant R155K in complex with danoprevir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M5MPDB ENTRY 3M5M CHAIN B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop, vapor diffusion6.229520-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3447.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.279α = 90
b = 58.537β = 90
c = 60.599γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-03-09SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-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
11.1595097.90.05511.25.867429
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)
11.1591.290.40.4714.76150

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 3M5M CHAIN B1.15940.8467223339197.610.15370.15270.1718RANDOM12.6627
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]
0.09-0.710.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.056
r_dihedral_angle_4_deg14.209
r_dihedral_angle_3_deg12.592
r_dihedral_angle_1_deg6.61
r_scangle_it3.63
r_scbond_it2.515
r_mcangle_it1.806
r_angle_refined_deg1.323
r_mcbond_it1.118
r_angle_other_deg1.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.056
r_dihedral_angle_4_deg14.209
r_dihedral_angle_3_deg12.592
r_dihedral_angle_1_deg6.61
r_scangle_it3.63
r_scbond_it2.515
r_mcangle_it1.806
r_angle_refined_deg1.323
r_mcbond_it1.118
r_angle_other_deg1.083
r_rigid_bond_restr0.941
r_mcbond_other0.372
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1418
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms57

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction