2FNT

Crystal structure of a drug-resistant (V82A) inactive (D25N) HIV-1 protease complexed with AP2V variant of HIV-1 NC-p1 substrate.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298126mM Sodium phosphate pH 6.2; 63mM sodium citrate; ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9938.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.056α = 90
b = 57.623β = 90
c = 61.475γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCD2003-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
11.44501000.0470.04710.493315533155

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1T3R1.4441.883315531723166299.580.188290.188290.186980.2137RANDOM17.784
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]
-1.03-0.221.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.703
r_dihedral_angle_4_deg14.237
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg7.2
r_scangle_it2.643
r_scbond_it1.886
r_angle_refined_deg1.32
r_mcangle_it1.2
r_mcbond_it0.962
r_angle_other_deg0.665
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.703
r_dihedral_angle_4_deg14.237
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg7.2
r_scangle_it2.643
r_scbond_it1.886
r_angle_refined_deg1.32
r_mcangle_it1.2
r_mcbond_it0.962
r_angle_other_deg0.665
r_xyhbond_nbd_refined0.264
r_symmetry_vdw_other0.237
r_symmetry_hbond_refined0.222
r_mcbond_other0.221
r_nbd_refined0.208
r_nbd_other0.194
r_symmetry_vdw_refined0.19
r_nbtor_refined0.175
r_nbtor_other0.088
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms1734
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing