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Crystal structure of the BCL6 BTB domain in complex with OICR-12694
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.2 293 10% PEG 6000, 0.1M Acetate:MES buffer pH 5.2, 10% DMSO, 50 mM CaCl2 with microseeding
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.786 α = 90 b = 72.939 β = 106.32 c = 55.336 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 2017-02-26 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 1.3 53.11 97 0.066 0.075 0.035 0.997 9.4 4.4 57693 10.4
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 1.3 1.32 94.5 0.432 0.495 0.237 0.868 2.9 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 FREE R-VALUE 3LB7 1.3 53.11 1.96 57180 2853 96.11 0.1462 0.1442 0.1454 0.1836 0.185
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 25.479 f_angle_d 1.261 f_chiral_restr 0.076 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1950 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing