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Crystal structure of the BCL6 BTB domain in complex with Compound 1a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Bis-Tris, potassium/sodium tartrate
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.618 α = 90 b = 66.618 β = 90 c = 151.996 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2014-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.58 50 98.8 0.063 26.8 9.2 27912
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 95.5 0.78 1.7 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1R28 1.58 40 26383 1390 98.68 0.20001 0.19929 0.21329 0.2495 RANDOM 27.751
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] 0.18 0.09 0.18 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.472 r_dihedral_angle_4_deg 16.758 r_dihedral_angle_3_deg 13.328 r_long_range_B_refined 5.098 r_long_range_B_other 4.944 r_dihedral_angle_1_deg 4.887 r_scangle_other 2.557 r_mcangle_it 1.97 r_mcangle_other 1.969 r_angle_refined_deg 1.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.472 r_dihedral_angle_4_deg 16.758 r_dihedral_angle_3_deg 13.328 r_long_range_B_refined 5.098 r_long_range_B_other 4.944 r_dihedral_angle_1_deg 4.887 r_scangle_other 2.557 r_mcangle_it 1.97 r_mcangle_other 1.969 r_angle_refined_deg 1.643 r_scbond_it 1.548 r_scbond_other 1.545 r_mcbond_it 1.126 r_mcbond_other 1.126 r_angle_other_deg 0.987 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1042 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing