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Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 75 mM NaAcetate, 900 mM K2HPO4, 700 NaH2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.87 68.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.55 α = 90 b = 150.55 β = 90 c = 312.25 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 315 2004-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
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 2.6 48.7 97 0.07 20 12.3 65050 63099
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) 2.6 2.72 98.5 0.54 5.3 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1R29 2.6 48.7 65050 63035 3069 97.06 0.221 0.219 0.2158 0.26 0.2567 RANDOM 71.704
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] -1.62 -0.81 -1.62 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.1 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 20.349 r_dihedral_angle_1_deg 7.098 r_scangle_it 4.703 r_scbond_it 2.858 r_mcangle_it 2.275 r_angle_refined_deg 1.783 r_mcbond_it 1.629 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.1 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 20.349 r_dihedral_angle_1_deg 7.098 r_scangle_it 4.703 r_scbond_it 2.858 r_mcangle_it 2.275 r_angle_refined_deg 1.783 r_mcbond_it 1.629 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.307 r_nbd_refined 0.25 r_symmetry_hbond_refined 0.249 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8950 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection