☰ Navigation Tabs
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 1.95 37.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.2 α = 90 b = 48.2 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 1.95 50 95.1 0.058 0.045 23.8 5.7 19634 18720 39.7
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 2.05 87 0.344 0.416 4.6 5.7 2380
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.95 38.72 18517 975 100 0.20538 0.20288 0.25349 0.227 RANDOM 36.152
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 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 23.778 r_dihedral_angle_3_deg 17.625 r_dihedral_angle_1_deg 6.887 r_scangle_it 5.245 r_scbond_it 3.436 r_mcangle_it 2.521 r_angle_refined_deg 2.154 r_mcbond_it 1.457 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 23.778 r_dihedral_angle_3_deg 17.625 r_dihedral_angle_1_deg 6.887 r_scangle_it 5.245 r_scbond_it 3.436 r_mcangle_it 2.521 r_angle_refined_deg 2.154 r_mcbond_it 1.457 r_chiral_restr 0.134 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 2095 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 53
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling