3EKY

Crystal Structure of wild-type HIV protease in complex with the inhibitor, Atazanavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F7APDB ENTRY 1F7A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2300126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.1241.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.862α = 90
b = 58.099β = 90
c = 61.999γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVYale mirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.85095.70.0710.0718.96.816904

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 1F7A1.842.411600386195.650.177390.175660.20857RANDOM17.92
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]
0.080.26-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.034
r_dihedral_angle_4_deg14.01
r_dihedral_angle_3_deg11.552
r_dihedral_angle_1_deg5.896
r_scangle_it1.53
r_angle_refined_deg1.179
r_scbond_it1.026
r_angle_other_deg0.704
r_mcangle_it0.596
r_mcbond_it0.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.034
r_dihedral_angle_4_deg14.01
r_dihedral_angle_3_deg11.552
r_dihedral_angle_1_deg5.896
r_scangle_it1.53
r_angle_refined_deg1.179
r_scbond_it1.026
r_angle_other_deg0.704
r_mcangle_it0.596
r_mcbond_it0.431
r_symmetry_vdw_refined0.281
r_nbd_refined0.181
r_nbd_other0.173
r_nbtor_refined0.164
r_symmetry_vdw_other0.163
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.125
r_mcbond_other0.101
r_nbtor_other0.077
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing