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Crystal structure of the BCL6 BTB domain in complex with OICR-8446
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, HANGING DROP 4.8 292 sodium formate, sodium acetate, pH 4.8
Crystal Properties Matthews coefficient Solvent content 2.04 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.768 α = 90 b = 72.771 β = 107.485 c = 55.706 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 2012-06-16 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 1.45 27.54 97.8 0.04 0.054 0.032 0.99 17.4 4.3 20085 17.99
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 1.45 1.53 99.1 0.445 0.578 0.364 2.9 4.3
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 1R29 1.45 27.54 1.76 19576 1003 95.2 0.1587 0.158 0.1583 0.1701 0.1685 28.7
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 13.6641 f_angle_d 1.4662 f_chiral_restr 0.0939 f_bond_d 0.0145 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 974 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing