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Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZSQ PDB ENTRY 3ZSQ
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 2.95 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.16 α = 90 b = 71.16 β = 90 c = 67.08 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 2009-03-31 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 1.71 45.4 100 0.09 12.9 5.6 41142
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 1.71 1.8 100 0.32 4.8 5.4
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 3ZSQ 1.71 31.45 38971 2057 99.9 0.18014 0.17938 0.1892 0.19423 0.2033 RANDOM 24.596
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 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.914 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_4_deg 9.858 r_dihedral_angle_1_deg 5.344 r_mcangle_it 2.655 r_scbond_it 1.655 r_mcbond_it 1.519 r_mcbond_other 1.519 r_angle_refined_deg 1.141 r_angle_other_deg 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.914 r_dihedral_angle_3_deg 12.446 r_dihedral_angle_4_deg 9.858 r_dihedral_angle_1_deg 5.344 r_mcangle_it 2.655 r_scbond_it 1.655 r_mcbond_it 1.519 r_mcbond_other 1.519 r_angle_refined_deg 1.141 r_angle_other_deg 0.77 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_it 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 2312 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing