4OBK

Crystal structure of inactive HIV-1 protease in complex with the P1-P6 substrate variant (L449F/S451N)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T3RPDB entry 1T3R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52951.0M Ammonium sulphate, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
238.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.945α = 90
b = 58.412β = 90
c = 61.457γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirrors2009-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.033APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.655098.10.08620.227222932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7198.10.4145.396.8

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 1T3R1.6530.7321058114697.70.181550.179970.21081RANDOM16.85
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]
-1.02-0.071.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.82
r_dihedral_angle_4_deg13.571
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg6.557
r_scbond_it2.494
r_mcangle_it2.007
r_angle_refined_deg1.589
r_mcbond_it1.317
r_mcbond_other1.211
r_angle_other_deg0.708
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.82
r_dihedral_angle_4_deg13.571
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg6.557
r_scbond_it2.494
r_mcangle_it2.007
r_angle_refined_deg1.589
r_mcbond_it1.317
r_mcbond_other1.211
r_angle_other_deg0.708
r_chiral_restr0.099
r_gen_planes_refined0.011
r_bond_refined_d0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1573
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BioCARS-developeddata collection
HKL-2000data reduction
HKL-2000data scaling