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Crystal structure of the BCL6 BTB domain in complex with OICR-9287
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 292 Precipitant solution was 16-20% PEG 8K in 0.1M pH 6.5 Hepes buffer, 50 mM CaCl2 with microseeding. Crystals were soaked in 0.1M Hepes 7.4, 20% PEG 8K, 25% glycerol 0.5 mM ligand prior to passage through paratone and freezing. Crystals grew as large doubly birefringent rods which were gently crushed. Singly birefringent pieces were selected for data collection.
Crystal Properties Matthews coefficient Solvent content 2.01 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.62 α = 90 b = 72.198 β = 105.97 c = 55.079 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 2013-08-10 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) 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 2.21 52.95 99.6 0.094 0.131 0.09 9 3.3 5769 28.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.37 0.483 0.665 0.456 2.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1R29 2.21 36.1 5769 576 99.33 0.1688 0.1626 0.1641 0.2259 0.2256 33.37
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 18.1202 f_angle_d 1.2347 f_chiral_restr 0.0843 f_bond_d 0.0134 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 981 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing