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Crystal structure of the BCL6 BTB domain in complex with OICR-10269
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 Microseeding with10% 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 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.215 α = 90 b = 72.787 β = 105.72 c = 54.995 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 2014-08-02 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) 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 1.5 52.94 97.7 0.046 13.5 3.4 18489
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 1.5 1.505 96.5 0.648 0.6 0.525 0.726 2 3.3
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 1R29 1.5 30.01 17538 946 97.4 0.148 0.146 0.1484 0.178 0.1806 RANDOM 28.89
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] 0.07 0.47 -0.14 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.698 r_dihedral_angle_4_deg 17.804 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 5.411 r_angle_refined_deg 2.497 r_angle_other_deg 1.696 r_chiral_restr 0.146 r_bond_refined_d 0.022 r_gen_planes_refined 0.018 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.698 r_dihedral_angle_4_deg 17.804 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 5.411 r_angle_refined_deg 2.497 r_angle_other_deg 1.696 r_chiral_restr 0.146 r_bond_refined_d 0.022 r_gen_planes_refined 0.018 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing