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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 4.6 293 1.8M AmSO4, 0.15M Na CITRATE pH 4.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.16 α = 90 b = 49.16 β = 90 c = 103.12 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 ADSC QUANTUM 210r MIRRORS 2008-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.957 Australian Synchrotron MX1
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 1.8 50 99.4 0.037 0.041 27.7 5.6 25837 25677
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) 1.8 1.9 15 0.16 0.18 9.7 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3L3U 1.8 26.75 25837 24417 1285 100 0.18852 0.18702 0.2173 0.2245 RANDOM 25.29
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] 0.02 0.01 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.484 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_4_deg 8.066 r_dihedral_angle_1_deg 5.698 r_scangle_it 3.832 r_scbond_it 2.543 r_mcangle_it 1.962 r_angle_refined_deg 1.688 r_mcbond_it 1.186 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.484 r_dihedral_angle_3_deg 15.1 r_dihedral_angle_4_deg 8.066 r_dihedral_angle_1_deg 5.698 r_scangle_it 3.832 r_scbond_it 2.543 r_mcangle_it 1.962 r_angle_refined_deg 1.688 r_mcbond_it 1.186 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.175 r_metal_ion_refined 0.164 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2092 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 77
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling