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Structural basis for the recognition between HIV-1 integrase and LEDGF/p75
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BIS PDB Entry: 1BIS (Integrase), 1Z9E (LEDGF) experimental model PDB 1Z9E PDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 295 PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.12 41.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.421 α = 90 b = 60.593 β = 109.06 c = 71.126 γ = 90
Symmetry Space Group C 1 2 1
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 4 2005-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.00 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.02 50 99.2 0.072 18.9 4.8 32648 32136 3.1 3.1 35.2
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 2.02 2.09 99.2 99.2 0.47 3.1 4.5
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: 1BIS (Integrase), 1Z9E (LEDGF) 2.02 20 30406 32113 1627 99.19 0.183 0.183 0.181 0.1803 0.226 0.2238 RANDOM 37.386
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] 0.03 1.3 -0.38 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_1_deg 5.524 r_scangle_it 4.361 r_scbond_it 2.778 r_angle_refined_deg 1.602 r_mcangle_it 1.6 r_mcbond_it 0.981 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_1_deg 5.524 r_scangle_it 4.361 r_scbond_it 2.778 r_angle_refined_deg 1.602 r_mcangle_it 1.6 r_mcbond_it 0.981 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.132 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3503 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection CCP4 phasing