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Crystal structure of the BCL6 BTB domain in complex with OICR-7629
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 1.2 M Ammonium sulfate, 0.1 M citrate pH 5.6 with 0.5 mM compound
Crystal Properties Matthews coefficient Solvent content 1.98 37.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.606 α = 90 b = 72.113 β = 104.875 c = 55.044 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2011-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.17 53.2 96.65 0.023 0.031 0.017 0.995 21.5 3 37874 11.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.23 82.73 0.147 0.204 0.135 0.9 4.4 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3LBZ 1.17 29.85 1.38 37866 1864 96.65 0.1162 0.1154 0.1167 0.1313 0.1329 17.84
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.8458 f_angle_d 1.5108 f_chiral_restr 0.0872 f_bond_d 0.0162 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1010 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing