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Crystal structure of the BCL6 BTB domain in complex with a hybrid BTB-binding (HBP) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 9.9% (v/v) MPD, 2.64% (w/v), PEG 8000 0.5 M NaCl, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.657 α = 90 b = 47.3 β = 94.34 c = 76.37 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 PSI PILATUS 6M 2018-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9793 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.13 40.21 99.8 0.183 0.172 0.981 4.3 3.3 15991 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.19 100 0.386 3.1
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 1R2B 2.13 40.21 15123 851 99.32 0.2022 0.1993 0.2059 0.2495 0.2493 RANDOM 38.594
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] -0.04 0.22 -1.45 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.002 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_4_deg 12.899 r_dihedral_angle_1_deg 5.556 r_angle_refined_deg 1.271 r_angle_other_deg 0.897 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.002 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_4_deg 12.899 r_dihedral_angle_1_deg 5.556 r_angle_refined_deg 1.271 r_angle_other_deg 0.897 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2261 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing