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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, 0.15 M Na Citrate pH 4.6, 5 mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49 α = 90 b = 49 β = 90 c = 103.6 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 2008-08-16 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 1.9 50 96.8 0.041 0.046 26.6 5.7 21930 21222 32.6
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 91.8 0.288 0.318 6.2 5.7 2860
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 39.27 21222 20732 1092 100 0.18122 0.17811 0.1802 0.24111 0.2395 RANDOM 29.28
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] 1.3 0.65 1.3 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_3_deg 15.482 r_dihedral_angle_4_deg 11.441 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.173 r_scbond_it 3.274 r_mcangle_it 2.604 r_angle_refined_deg 2.075 r_mcbond_it 1.461 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_3_deg 15.482 r_dihedral_angle_4_deg 11.441 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.173 r_scbond_it 3.274 r_mcangle_it 2.604 r_angle_refined_deg 2.075 r_mcbond_it 1.461 r_chiral_restr 0.17 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2087 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 72
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling