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Fragments bound to 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 5.6 295 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.601 α = 90 b = 62.323 β = 90 c = 82.087 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 ADSC QUANTUM 210r 2007-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95 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 49.63 99.98 0.108 0.117 13.5 25133 25118
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99.98
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 (All) 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 49.63 25113 23866 1267 99.98 0.2085 0.21068 0.20846 0.2098 0.25118 0.2503 RANDOM 26.541
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] 0.42 0.74 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.658 r_dihedral_angle_3_deg 17.807 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_1_deg 6.601 r_scangle_it 3.997 r_scbond_it 3 r_mcangle_it 2.066 r_angle_refined_deg 1.917 r_mcbond_it 1.737 r_angle_other_deg 1.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.658 r_dihedral_angle_3_deg 17.807 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_1_deg 6.601 r_scangle_it 3.997 r_scbond_it 3 r_mcangle_it 2.066 r_angle_refined_deg 1.917 r_mcbond_it 1.737 r_angle_other_deg 1.124 r_symmetry_metal_ion_refined 0.977 r_metal_ion_refined 0.409 r_mcbond_other 0.351 r_symmetry_vdw_other 0.308 r_symmetry_hbond_refined 0.286 r_chiral_restr 0.255 r_symmetry_vdw_refined 0.241 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.214 r_nbd_other 0.202 r_nbtor_refined 0.177 r_nbtor_other 0.09 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other 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 2175 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 48
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling