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Crystal structure of the BCL6 BTB domain in complex with Compound 1
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 2.98 58.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.425 α = 90 b = 66.425 β = 90 c = 152.192 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 2014-02-27 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 1.65 50 99.8 0.057 36.2 12.4 24802
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 1.65 1.68 96.6 1.2
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 1.65 10 23303 1254 99.05 0.17986 0.1786 0.20568 0.2296 RANDOM 30.616
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] 0.32 0.16 0.32 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.264 r_dihedral_angle_4_deg 17.548 r_dihedral_angle_3_deg 14.222 r_long_range_B_refined 5.54 r_long_range_B_other 5.204 r_dihedral_angle_1_deg 4.847 r_scangle_other 3.455 r_scbond_it 2.149 r_scbond_other 2.147 r_mcangle_other 1.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.264 r_dihedral_angle_4_deg 17.548 r_dihedral_angle_3_deg 14.222 r_long_range_B_refined 5.54 r_long_range_B_other 5.204 r_dihedral_angle_1_deg 4.847 r_scangle_other 3.455 r_scbond_it 2.149 r_scbond_other 2.147 r_mcangle_other 1.993 r_mcangle_it 1.992 r_angle_refined_deg 1.52 r_mcbond_it 1.239 r_mcbond_other 1.231 r_angle_other_deg 1.111 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 98 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing