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Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 mM TRIS PH 8.0, 250 mM NACL, 30 mM MGCL2, 5 mM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 mM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.492 α = 90 b = 71.492 β = 90 c = 67.357 γ = 120
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 210 2009-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON 0.95661 Australian Synchrotron MX1
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 1.7 45.6 99.9 0.074 14 5.6 42336
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 1.7 1.79 0.753 2 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.7 45.62 40069 2137 99.66 0.20017 0.19938 0.2072 0.21478 0.223 RANDOM 26.766
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 0.03 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.281 r_dihedral_angle_3_deg 13.497 r_dihedral_angle_4_deg 8.144 r_long_range_B_refined 6.011 r_long_range_B_other 6.01 r_dihedral_angle_1_deg 5.065 r_scangle_other 3.309 r_mcangle_it 2.979 r_mcangle_other 2.978 r_scbond_it 2.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.281 r_dihedral_angle_3_deg 13.497 r_dihedral_angle_4_deg 8.144 r_long_range_B_refined 6.011 r_long_range_B_other 6.01 r_dihedral_angle_1_deg 5.065 r_scangle_other 3.309 r_mcangle_it 2.979 r_mcangle_other 2.978 r_scbond_it 2.008 r_scbond_other 2.007 r_mcbond_it 1.707 r_mcbond_other 1.699 r_angle_refined_deg 1.404 r_angle_other_deg 0.753 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2318 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement