3OXX

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


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
2.1442.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.238α = 90
b = 58.489β = 95.88
c = 62.118γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSi (111) double-crystal monochromator, KB Mirror system2009-11-07SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.03APS14-ID-B

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
11.655096.30.05513.13.842578
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)
11.651.7199.80.3353.8

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 1TSU1.6527.7140294215595.760.174860.172710.21524RANDOM22.008
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]
-1.720.030.521.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.764
r_dihedral_angle_4_deg18.277
r_dihedral_angle_3_deg10.958
r_dihedral_angle_1_deg6.101
r_scangle_it3.63
r_scbond_it2.291
r_angle_other_deg2.219
r_angle_refined_deg1.434
r_mcangle_it1.394
r_mcbond_it0.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.764
r_dihedral_angle_4_deg18.277
r_dihedral_angle_3_deg10.958
r_dihedral_angle_1_deg6.101
r_scangle_it3.63
r_scbond_it2.291
r_angle_other_deg2.219
r_angle_refined_deg1.434
r_mcangle_it1.394
r_mcbond_it0.826
r_mcbond_other0.133
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.003
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 Atoms2935
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms179

Software

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