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Crystal structure of the BCL6 BTB domain in complex with OICR-10268
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 4.6 292 10% PEG6K with 0.1M MES pH 4.6, 100 mM AmSO4, 10% glycerol, 10% DMSO in Reservoir. Shifted to pH 7.4, 20% glycerol for freezing
Crystal Properties Matthews coefficient Solvent content 2.03 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.768 α = 90 b = 72.566 β = 105.85 c = 55.128 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 2014-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 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 1.25 36.28 96.7 0.034 0.041 0.022 0.999 16.6 3.4 30799
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 1.25 1.35 95.2 0.445 0.529 0.283 0.859 3.4
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 1R_29 1.25 36.28 29322 1477 96.53 0.1377 0.1365 0.1382 0.1623 0.1638 RANDOM 24.954
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] -0.02 -0.04 0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.052 r_sphericity_free 27.357 r_dihedral_angle_4_deg 20.363 r_sphericity_bonded 17.76 r_dihedral_angle_3_deg 12.186 r_dihedral_angle_1_deg 4.975 r_rigid_bond_restr 2.994 r_angle_refined_deg 1.554 r_angle_other_deg 0.821 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.052 r_sphericity_free 27.357 r_dihedral_angle_4_deg 20.363 r_sphericity_bonded 17.76 r_dihedral_angle_3_deg 12.186 r_dihedral_angle_1_deg 4.975 r_rigid_bond_restr 2.994 r_angle_refined_deg 1.554 r_angle_other_deg 0.821 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 985 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 83
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing