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Crystal structure of the BCL6 BTB domain in complex with Compound 5
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 59.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.55 α = 90 b = 66.55 β = 90 c = 153.09 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 2014-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
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 1.86 50 96.6 0.063 37.8 10.6 17116
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 1.86 1.89 98.5 1 2 10.8
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 1.86 40 16233 866 96.86 0.1911 0.18888 0.23463 0.2429 RANDOM 42.73
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] 0.16 0.08 0.16 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 17.603 r_dihedral_angle_3_deg 14.854 r_dihedral_angle_1_deg 5.807 r_long_range_B_refined 5.184 r_long_range_B_other 5.169 r_scangle_other 3.754 r_mcangle_it 2.609 r_mcangle_other 2.608 r_scbond_it 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.416 r_dihedral_angle_4_deg 17.603 r_dihedral_angle_3_deg 14.854 r_dihedral_angle_1_deg 5.807 r_long_range_B_refined 5.184 r_long_range_B_other 5.169 r_scangle_other 3.754 r_mcangle_it 2.609 r_mcangle_other 2.608 r_scbond_it 2.266 r_scbond_other 2.259 r_angle_refined_deg 1.695 r_mcbond_other 1.648 r_mcbond_it 1.647 r_angle_other_deg 1.017 r_chiral_restr 0.086 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 1050 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing