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Crystal structure of the HIV-1 integrase core domain to 1.4A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EXQ PDB ENTRY 1exq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1.8M Ammonium sulfate, 0.15M sodium citrate, 5mM cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.55 α = 90 b = 62.434 β = 90 c = 81.127 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 315 2006-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.900020 APS 14-BM-C
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 1.4 34.015 99.8 0.112 0.112 15.2 12.5 60131 60131 11.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 100 0.439 6.6 13.3 8679
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1exq 1.4 34.01 2 60063 3064 99.7 0.205 0.204 0.1839 0.236 0.2244 RANDOM 11.97
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] 0.41 -0.22 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.881 r_dihedral_angle_4_deg 20.622 r_dihedral_angle_3_deg 13.449 r_scangle_it 7.227 r_dihedral_angle_1_deg 5.936 r_scbond_it 5.075 r_mcangle_it 3.246 r_mcbond_it 2.198 r_rigid_bond_restr 2.139 r_angle_refined_deg 2.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.881 r_dihedral_angle_4_deg 20.622 r_dihedral_angle_3_deg 13.449 r_scangle_it 7.227 r_dihedral_angle_1_deg 5.936 r_scbond_it 5.075 r_mcangle_it 3.246 r_mcbond_it 2.198 r_rigid_bond_restr 2.139 r_angle_refined_deg 2.079 r_angle_other_deg 1.106 r_mcbond_other 0.734 r_chiral_restr 0.136 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2263 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 15
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction