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Crystal structure of the BCL6 BTB domain in complex with OICR-12387
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 VAPOR DIFFUSION, SITTING DROP 5.3 290 9% PEG6K as precipitant in pH 5.3 MES buffer with 10% DMSO and 100 mM NH4SO4
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.484 α = 90 b = 72.545 β = 109.15 c = 67.488 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 PILATUS 6M 2016-10-16 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 1.49 63.75 99.8 0.099 0.112 0.052 0.997 9.6 4.4 82198 13.72
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 1.49 1.57 99.7 0.745 0.852 0.407 0.764 4.2
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 THROUGHOUT 1R29 1.49 36.27 1.35 82134 3969 99.75 0.1425 0.1406 0.1411 0.1799 0.1789 21.5899
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 12.949 f_angle_d 1.241 f_chiral_restr 0.095 f_bond_d 0.018 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3924 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 386
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction