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Crystal structure of the BCL6 BTB domain in complex with F1324(10-13)
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 8 293 0.1M Tris pH 8.0, 0.6M potassium/sodium tartrate
Crystal Properties Matthews coefficient Solvent content 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.398 α = 90 b = 67.398 β = 90 c = 166.725 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 2014-02-14 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 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 1.95 50 96.4 0.076 31.2 10.3 16594
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 1.95 2 97.8 0.341 2.6 10
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 1.95 40 15736 783 96.34 0.19209 0.19048 0.22656 0.2436 RANDOM 40.799
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] -0.45 -0.23 -0.45 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.782 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 5.669 r_long_range_B_refined 5.42 r_long_range_B_other 5.336 r_scangle_other 2.534 r_mcangle_it 2.108 r_mcangle_other 2.108 r_scbond_it 1.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.782 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 5.669 r_long_range_B_refined 5.42 r_long_range_B_other 5.336 r_scangle_other 2.534 r_mcangle_it 2.108 r_mcangle_other 2.108 r_scbond_it 1.526 r_scbond_other 1.522 r_angle_refined_deg 1.409 r_mcbond_it 1.254 r_mcbond_other 1.253 r_angle_other_deg 0.938 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 1128 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing