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HIV-1 IN core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BL3 PDB ENTRY 1bl3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.4M SODIUM CITRATE, 50mM HEPES PH 7.5, 7.5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.327 α = 90 b = 72.909 β = 108.6 c = 79.851 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 MARMOSAIC 300 mm CCD 2007-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94937 APS 23-ID-B
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 75.6 99.52 0.051 0.051 17.5 3.7 42674 42469 2 2
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 1.9 2 99.6 0.299 0.299 2.5
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 1bl3 1.9 75.59 42469 40326 2143 99.52 0.1958 0.1976 0.19578 0.1962 0.23202 0.2355 RANDOM 27.056
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] 1.77 0.55 -0.04 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.579 r_dihedral_angle_4_deg 14.37 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 4.949 r_scangle_it 4.535 r_angle_other_deg 4.118 r_scbond_it 3.004 r_mcangle_it 2.141 r_mcbond_it 1.243 r_angle_refined_deg 1.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.579 r_dihedral_angle_4_deg 14.37 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 4.949 r_scangle_it 4.535 r_angle_other_deg 4.118 r_scbond_it 3.004 r_mcangle_it 2.141 r_mcbond_it 1.243 r_angle_refined_deg 1.144 r_nbd_other 0.255 r_symmetry_vdw_other 0.232 r_nbd_refined 0.213 r_nbtor_refined 0.187 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.138 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.11 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 3419 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 11
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling