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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 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.032 α = 90 b = 49.032 β = 90 c = 103.724 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 1.8 50.8 99 0.055 0.06 23.1 5.6 25903 25633
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 1.9 100 0.264 0.294 4.9 4.9
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 1.8 34.57 25903 24362 1283 99.16 0.24558 0.24331 0.242 0.28898 0.2831 RANDOM 24.804
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] 0.85 0.43 0.85 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.402 r_dihedral_angle_3_deg 15.796 r_dihedral_angle_4_deg 15.598 r_dihedral_angle_1_deg 5.3 r_scangle_it 4.805 r_scbond_it 3.795 r_mcangle_it 3.417 r_mcbond_it 2.592 r_angle_refined_deg 1.493 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.402 r_dihedral_angle_3_deg 15.796 r_dihedral_angle_4_deg 15.598 r_dihedral_angle_1_deg 5.3 r_scangle_it 4.805 r_scbond_it 3.795 r_mcangle_it 3.417 r_mcbond_it 2.592 r_angle_refined_deg 1.493 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 2108 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 93
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing PHENIX refinement MOSFLM data reduction SCALA data scaling REFMAC refinement