4OBF

Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease Variant (D30N/N88D) in Complex with the p1-p6 substrate variant (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 DROP6.229532% Ammonium Sulphate, 63mM Sodium Citrate, 126mM Sodium Phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0238.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.547α = 90
b = 60.074β = 99.25
c = 60.232γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2009-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
11.685099.80.06621.124.1412652
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)
11.681.741000.7131.954

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 1T3R1.683039171207699.560.182170.179740.22889RANDOM28.068
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]
-2.41-0.330.771.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.275
r_dihedral_angle_4_deg14.196
r_dihedral_angle_3_deg13.281
r_dihedral_angle_1_deg7.107
r_scangle_it5.025
r_scbond_it3.251
r_mcangle_it2.227
r_angle_refined_deg1.46
r_mcbond_it1.367
r_angle_other_deg0.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.275
r_dihedral_angle_4_deg14.196
r_dihedral_angle_3_deg13.281
r_dihedral_angle_1_deg7.107
r_scangle_it5.025
r_scbond_it3.251
r_mcangle_it2.227
r_angle_refined_deg1.46
r_mcbond_it1.367
r_angle_other_deg0.806
r_mcbond_other0.42
r_chiral_restr0.097
r_gen_planes_refined0.011
r_bond_refined_d0.01
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_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 Atoms3083
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms74

Software

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