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Crystal Structure of the HIV-1 Integrase catalytic domain with GSK1264
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 7% Peg 8K, 0.2M Ammonium Sulfate, 0.1M sodiium cacodylate pH 6.5, 5mM MgCl2, 5mM MnCl2, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.664 α = 90 b = 72.664 β = 90 c = 65.453 γ = 120
Symmetry Space Group P 31 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 2013-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.82 50 98.1 0.044 18.2 8.3 18314 17966 -3 -3 30.1
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 1.82 1.89 98 0.41 8.5 1746
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 1.82 28.37 -3 18314 17396 572 98.24 0.1893 0.1889 0.2023 0.2008 0.2076 RANDOM 42.944
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] 0.29 0.29 0.29 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_3_deg 12.916 r_dihedral_angle_4_deg 7.715 r_dihedral_angle_1_deg 4.839 r_mcangle_it 2.144 r_mcbond_other 1.282 r_mcbond_it 1.281 r_angle_refined_deg 1.199 r_angle_other_deg 0.731 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_3_deg 12.916 r_dihedral_angle_4_deg 7.715 r_dihedral_angle_1_deg 4.839 r_mcangle_it 2.144 r_mcbond_other 1.282 r_mcbond_it 1.281 r_angle_refined_deg 1.199 r_angle_other_deg 0.731 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 983 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 44
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing