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Crystal structure of the BCL6 BTB domain in complex with F1324
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 0.1M imidazole pH 6.5, 0.2M lithium sulfate, 25% PEG 3350, 15% MPD
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.797 α = 90 b = 37.516 β = 112.94 c = 82.594 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 2013-09-27 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 Merge 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 1.85 50 92.1 0.095 10.5 3 23655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 54.3 0.606 1.3 2.4
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 1.85 40 22351 1143 92.47 0.24552 0.24357 0.249 0.28453 0.2932 RANDOM 28.247
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] -0.71 0.13 -0.39 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.506 r_dihedral_angle_4_deg 17.437 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_1_deg 5.883 r_long_range_B_refined 3.331 r_long_range_B_other 3.295 r_angle_refined_deg 1.405 r_mcangle_it 1.168 r_mcangle_other 1.168 r_scangle_other 1.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.506 r_dihedral_angle_4_deg 17.437 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_1_deg 5.883 r_long_range_B_refined 3.331 r_long_range_B_other 3.295 r_angle_refined_deg 1.405 r_mcangle_it 1.168 r_mcangle_other 1.168 r_scangle_other 1.121 r_angle_other_deg 0.974 r_scbond_it 0.682 r_scbond_other 0.682 r_mcbond_it 0.661 r_mcbond_other 0.661 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 2194 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing