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X-ray crystal structure of HIV-1 Protease T80S variant in complex with the inhibitor saquinavir used to explore the role of invariant Thr80 in HIV-1 protease structure, function, and viral infectivity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A pdb entry 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.126 M Sodium Phosphate pH 6.2, 0.063 M Sodium Citrate, 23-24% Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.5 α = 90 b = 57.93 β = 90 c = 61.62 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2004-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 42.22 99.1 0.073 0.073 8.2 7 12625 12625
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1F7A 2 42.22 12625 11977 612 99.09 0.1791 0.17911 0.1764 0.23235 0.1874 RANDOM 21.948
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] -0.73 0.52 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.207 r_dihedral_angle_4_deg 27.859 r_dihedral_angle_3_deg 12.644 r_dihedral_angle_1_deg 6.942 r_scangle_it 3.321 r_scbond_it 2.217 r_angle_refined_deg 1.613 r_mcangle_it 1.443 r_mcbond_it 1.2 r_angle_other_deg 0.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.207 r_dihedral_angle_4_deg 27.859 r_dihedral_angle_3_deg 12.644 r_dihedral_angle_1_deg 6.942 r_scangle_it 3.321 r_scbond_it 2.217 r_angle_refined_deg 1.613 r_mcangle_it 1.443 r_mcbond_it 1.2 r_angle_other_deg 0.679 r_mcbond_other 0.263 r_symmetry_hbond_refined 0.216 r_nbd_other 0.213 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.19 r_symmetry_vdw_other 0.177 r_nbtor_refined 0.176 r_chiral_restr 0.093 r_nbtor_other 0.092 r_xyhbond_nbd_other 0.073 r_symmetry_vdw_refined 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1462 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing