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Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L3U PDB ENTRY 3L3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.587 α = 90 b = 61.997 β = 90 c = 81.765 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 MAR scanner 300 mm plate double crystal monochromator and K-B pair of biomorph mirrors 2007-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97937 APS 23-ID-B
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 1.9 62 99.9 0.086 0.093 11 7 24972 24930
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 100 0.48 0.52 3.2 7
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 (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 3L3U 1.9 49.4 24930 23602 1234 99.67 0.21876 0.21635 0.2132 0.2676 0.2649 RANDOM 38.818
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] -0.33 2.64 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.015 r_dihedral_angle_3_deg 14.597 r_dihedral_angle_4_deg 12.575 r_dihedral_angle_1_deg 4.863 r_scangle_it 4.325 r_mcangle_it 3.119 r_scbond_it 3.05 r_mcbond_it 2.152 r_angle_refined_deg 1.374 r_symmetry_hbond_refined 0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.015 r_dihedral_angle_3_deg 14.597 r_dihedral_angle_4_deg 12.575 r_dihedral_angle_1_deg 4.863 r_scangle_it 4.325 r_mcangle_it 3.119 r_scbond_it 3.05 r_mcbond_it 2.152 r_angle_refined_deg 1.374 r_symmetry_hbond_refined 0.386 r_metal_ion_refined 0.254 r_symmetry_vdw_other 0.249 r_nbd_refined 0.204 r_nbd_other 0.186 r_mcbond_other 0.184 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.114 r_nbtor_other 0.083 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_xyhbond_nbd_other 0.004 r_gen_planes_other 0.001 r_bond_other_d r_angle_other_deg 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 2159 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 39
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling