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HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Sodium Fluoride, 0.1 M bis-Tris propane, pH 8.5 and 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.181 α = 90 b = 54.814 β = 91.23 c = 117.996 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2012-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.05 54.81 97.1 0.097 8.6 2.4 55617 28.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 97 0.796 0.51 1.7 2.4
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 2b4j 2.05 14.98 52601 2800 96.29 0.18506 0.1823 0.1885 0.23628 0.2415 RANDOM 37.998
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] 0.01 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.905 r_dihedral_angle_4_deg 16.502 r_dihedral_angle_3_deg 14.821 r_long_range_B_refined 9.207 r_long_range_B_other 9.187 r_scangle_other 7.24 r_dihedral_angle_1_deg 5.298 r_mcangle_it 4.921 r_mcangle_other 4.92 r_scbond_it 4.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.905 r_dihedral_angle_4_deg 16.502 r_dihedral_angle_3_deg 14.821 r_long_range_B_refined 9.207 r_long_range_B_other 9.187 r_scangle_other 7.24 r_dihedral_angle_1_deg 5.298 r_mcangle_it 4.921 r_mcangle_other 4.92 r_scbond_it 4.714 r_scbond_other 4.713 r_mcbond_it 3.359 r_mcbond_other 3.354 r_angle_refined_deg 1.877 r_angle_other_deg 1.044 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5606 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing