☰ Navigation Tabs
GS-8374, a Novel Phosphonate-Containing Inhibitor of HIV-1 Protease, Effectively Inhibits HIV PR Mutants with Amino Acid Insertions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RKF PDB ENTRY 2RKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292.15 0.5 M ammonium sulphate and 0.1 M sodium acetate pH 5.25-5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.756 α = 90 b = 61.756 β = 90 c = 83.352 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 11333 10764
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2RKF 2.05 53.45 10832 10764 538 99.37 0.20339 0.20339 0.20069 0.2095 0.26576 0.2613 RANDOM 55.426
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] 0.13 0.07 0.13 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.345 r_dihedral_angle_4_deg 19.789 r_dihedral_angle_3_deg 15.206 r_dihedral_angle_1_deg 6.235 r_scangle_it 3.642 r_scbond_it 2.141 r_mcangle_it 1.97 r_angle_refined_deg 1.695 r_mcbond_it 1.056 r_angle_other_deg 0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.345 r_dihedral_angle_4_deg 19.789 r_dihedral_angle_3_deg 15.206 r_dihedral_angle_1_deg 6.235 r_scangle_it 3.642 r_scbond_it 2.141 r_mcangle_it 1.97 r_angle_refined_deg 1.695 r_mcbond_it 1.056 r_angle_other_deg 0.923 r_mcbond_other 0.148 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement