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Crystal structure of the BCL6 BTB domain in complex with Compound 7
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 3.05 59.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.874 α = 90 b = 66.874 β = 90 c = 153.781 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 2015-03-09 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 2 50 100 0.067 29 11.1 14486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 1.3 9.4
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 1R28 2 40 13687 731 99.6 0.19969 0.19802 0.2044 0.23035 0.242 RANDOM 53.4
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 -0.02 -0.04 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.394 r_dihedral_angle_4_deg 15.547 r_dihedral_angle_3_deg 13.872 r_long_range_B_other 6.246 r_long_range_B_refined 6.245 r_dihedral_angle_1_deg 5.684 r_scangle_other 3.949 r_mcangle_it 3.164 r_mcangle_other 3.162 r_scbond_it 2.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.394 r_dihedral_angle_4_deg 15.547 r_dihedral_angle_3_deg 13.872 r_long_range_B_other 6.246 r_long_range_B_refined 6.245 r_dihedral_angle_1_deg 5.684 r_scangle_other 3.949 r_mcangle_it 3.164 r_mcangle_other 3.162 r_scbond_it 2.372 r_scbond_other 2.368 r_mcbond_other 1.964 r_mcbond_it 1.962 r_angle_refined_deg 1.534 r_angle_other_deg 0.977 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 31 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing