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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NF7 PDB ENTRY 3NF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 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 2.45 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.475 α = 90 b = 71.475 β = 90 c = 66.453 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 210r MIRRORS 2009-07-29 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 2 45.3 100 0.08 16.4 5.6 25674 1 27.12
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 2.11 100 0.55 3 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 3NF7 2 31.48 24345 1303 100 0.18842 0.18657 0.1841 0.22221 0.2214 RANDOM 26.833
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] 0.18 0.09 0.18 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.371 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_1_deg 6.036 r_scangle_it 3.678 r_scbond_it 2.588 r_mcangle_it 1.795 r_angle_refined_deg 1.618 r_mcbond_it 1.363 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.371 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_1_deg 6.036 r_scangle_it 3.678 r_scbond_it 2.588 r_mcangle_it 1.795 r_angle_refined_deg 1.618 r_mcbond_it 1.363 r_nbtor_refined 0.301 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.076 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 96 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing