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Crystal Structure of Lysine Sulfonamide Inhibitor Reveals the Displacement of the Conserved Flap Water Molecule in HIV-1 Protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 126 mM sodium phosphate; 63 mM sodium citrate; 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.105 α = 90 b = 58.097 β = 90 c = 61.601 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 200 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2005-11-15 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 50 99.2 0.72 0.72 13.1 6.3 12879
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1F7A 2 42.26 12220 619 98.82 0.18898 0.18676 0.1986 0.2323 0.2483 RANDOM 24.819
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] -1.1 -0.32 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.808 r_dihedral_angle_4_deg 14.96 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 6.588 r_scangle_it 2.208 r_scbond_it 1.519 r_angle_refined_deg 1.26 r_mcangle_it 0.96 r_mcbond_it 0.743 r_angle_other_deg 0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.808 r_dihedral_angle_4_deg 14.96 r_dihedral_angle_3_deg 12.364 r_dihedral_angle_1_deg 6.588 r_scangle_it 2.208 r_scbond_it 1.519 r_angle_refined_deg 1.26 r_mcangle_it 0.96 r_mcbond_it 0.743 r_angle_other_deg 0.647 r_symmetry_vdw_refined 0.289 r_symmetry_hbond_refined 0.282 r_symmetry_vdw_other 0.205 r_mcbond_other 0.196 r_nbd_other 0.188 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.175 r_nbd_refined 0.174 r_nbtor_other 0.085 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1490 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing