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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 = 70.813 α = 90 b = 70.813 β = 90 c = 67.132 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 2008-12-13 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 1.7 45.3 96.8 0.07 16.7 5.5 40132
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 80 0.47 2.6 4.2
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 1.7 31.31 38081 2021 96.75 0.18072 0.17979 0.1883 0.19805 0.2047 RANDOM 21.072
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] 0.12 0.12 0.12 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.952 r_dihedral_angle_4_deg 15.492 r_dihedral_angle_3_deg 12.3 r_dihedral_angle_1_deg 5.584 r_mcangle_it 1.932 r_scbond_it 1.2 r_mcbond_it 1.094 r_mcbond_other 1.094 r_angle_refined_deg 1.068 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.952 r_dihedral_angle_4_deg 15.492 r_dihedral_angle_3_deg 12.3 r_dihedral_angle_1_deg 5.584 r_mcangle_it 1.932 r_scbond_it 1.2 r_mcbond_it 1.094 r_mcbond_other 1.094 r_angle_refined_deg 1.068 r_angle_other_deg 0.78 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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 2318 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing