3OXW

Crystal Structure of HIV-1 I50V, A71V Protease in Complex with the Protease Inhibitor Darunavir


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2295126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.62α = 90
b = 63.344β = 97.33
c = 58.648γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Bent conical Si-mirror (Rh coated), Bent Ge(111) monochromatorSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
11.955099.60.0888.44.426676
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)
11.952.0299.50.374.5

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 1TSU1.9531.6725320133999.250.175360.173030.21841RANDOM29.073
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]
-2.18-0.230.891.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.734
r_dihedral_angle_4_deg18.453
r_dihedral_angle_3_deg13.559
r_dihedral_angle_1_deg7.48
r_scangle_it4.963
r_scbond_it3.106
r_mcangle_it2.282
r_angle_other_deg1.742
r_angle_refined_deg1.37
r_mcbond_it1.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.734
r_dihedral_angle_4_deg18.453
r_dihedral_angle_3_deg13.559
r_dihedral_angle_1_deg7.48
r_scangle_it4.963
r_scbond_it3.106
r_mcangle_it2.282
r_angle_other_deg1.742
r_angle_refined_deg1.37
r_mcbond_it1.331
r_mcbond_other0.204
r_chiral_restr0.088
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2978
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms151

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling