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Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 THE PROTEIN WAS CONCENTRATED TO 5.5MG/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, 100MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
Crystal Properties Matthews coefficient Solvent content 2.45 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.006 α = 90 b = 71.006 β = 90 c = 67.023 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 CCD MIRRORS 2009-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 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 1.95 45.3 99.7 0.08 15.6 4.6 27504 1 22.8
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 1.95 2.06 99.4 0.46 2.8 4
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 1.95 35.51 26077 1393 99.69 0.18642 0.18423 0.1837 0.22754 0.2253 RANDOM 23.43
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 0.15 0.29 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.062 r_dihedral_angle_4_deg 17.398 r_dihedral_angle_3_deg 14.26 r_dihedral_angle_1_deg 5.332 r_scangle_it 2.737 r_scbond_it 1.996 r_mcangle_it 1.481 r_angle_refined_deg 1.466 r_mcbond_it 1.137 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.062 r_dihedral_angle_4_deg 17.398 r_dihedral_angle_3_deg 14.26 r_dihedral_angle_1_deg 5.332 r_scangle_it 2.737 r_scbond_it 1.996 r_mcangle_it 1.481 r_angle_refined_deg 1.466 r_mcbond_it 1.137 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.25 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other 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 126 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing