4OBG

Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease (D30N/N88D) in Complex with the p1-p6 substrate.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529528% PEG 5000, 0.1M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0239.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.672α = 90
b = 60.114β = 99.09
c = 60.196γ = 90
Symmetry
Space GroupP 1 21 1

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
11.785099.20.06814.73.9342882
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)
11.781.8699.70.3553.883.7

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 1T3R1.785032455171197.750.203120.200390.25461RANDOM29.977
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]
-2.56-0.480.831.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.162
r_dihedral_angle_4_deg14.942
r_dihedral_angle_3_deg14.528
r_dihedral_angle_1_deg7.449
r_scangle_it5.048
r_scbond_it3.235
r_mcangle_it2.184
r_angle_refined_deg1.404
r_mcbond_it1.335
r_angle_other_deg0.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.162
r_dihedral_angle_4_deg14.942
r_dihedral_angle_3_deg14.528
r_dihedral_angle_1_deg7.449
r_scangle_it5.048
r_scbond_it3.235
r_mcangle_it2.184
r_angle_refined_deg1.404
r_mcbond_it1.335
r_angle_other_deg0.783
r_mcbond_other0.411
r_chiral_restr0.088
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_gen_planes_other0.001
r_bond_other_d
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 Atoms3060
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms62

Software

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