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Fragment-based approach to the design of ligands targeting a novel site on 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 2.05 39.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.75 α = 90 b = 59.704 β = 90 c = 81.818 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 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors 2007-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1 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 1.95 48.25 99.4 0.1 0.112 9.7 4.5 23203 21811 22.38
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) 1.95 2.06 99.4 0.497 0.479 2.9 4.6 3184
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 1.95 40.91 21811 20602 1117 98.83 0.21278 0.21084 0.2156 0.24882 0.2527 RANDOM 25.036
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] -0.83 3.24 -2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_3_deg 16.86 r_dihedral_angle_4_deg 11.879 r_dihedral_angle_1_deg 6.585 r_scangle_it 4.472 r_scbond_it 2.897 r_angle_refined_deg 2.174 r_mcangle_it 2.124 r_mcbond_it 1.189 r_angle_other_deg 1.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_3_deg 16.86 r_dihedral_angle_4_deg 11.879 r_dihedral_angle_1_deg 6.585 r_scangle_it 4.472 r_scbond_it 2.897 r_angle_refined_deg 2.174 r_mcangle_it 2.124 r_mcbond_it 1.189 r_angle_other_deg 1.062 r_mcbond_other 0.277 r_chiral_restr 0.112 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 61
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling