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The structure of BCL6 BTB (POZ) domain in complex with the ansamycin antibiotic rifabutin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2B PDB ENTRY 1R2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 20% PEG 6000, 100MM SODIUM CITRATE, PH 5.
Crystal Properties Matthews coefficient Solvent content 1.99 38.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.172 α = 90 b = 54.828 β = 95.21 c = 58.159 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2012-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 2.3 39.82 97 0.108 9.8 3 9168 4.1
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 2.3 2.38 97 0.518 4.1 2.9
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 PDB ENTRY 1R2B 2.3 57.92 9168 466 97.13 0.20193 0.19877 0.2025 0.26875 0.2699 RANDOM 29.366
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] 1.85 -0.01 -0.11 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.034 r_dihedral_angle_4_deg 19.575 r_dihedral_angle_3_deg 17.089 r_dihedral_angle_1_deg 6.623 r_mcangle_it 3.032 r_scbond_it 2.594 r_angle_refined_deg 1.875 r_mcbond_it 1.848 r_mcbond_other 1.84 r_angle_other_deg 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.034 r_dihedral_angle_4_deg 19.575 r_dihedral_angle_3_deg 17.089 r_dihedral_angle_1_deg 6.623 r_mcangle_it 3.032 r_scbond_it 2.594 r_angle_refined_deg 1.875 r_mcbond_it 1.848 r_mcbond_other 1.84 r_angle_other_deg 0.863 r_chiral_restr 0.171 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1969 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing