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Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD
Crystal Properties Matthews coefficient Solvent content 4.22 70.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.626 α = 90 b = 96.163 β = 90 c = 57.846 γ = 90
Symmetry Space Group C 2 2 21
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 2M 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.05 42.51 99.9 0.105 0.114 0.043 0.998 11.6 6.9 14808
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 99.9 0.821 0.887 0.332 0.915 2.3 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 5DYU 2.05 41.313 1.34 14661 773 99 0.2164 0.215 0.215 0.2477 0.2575
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.578 f_angle_d 0.802 f_chiral_restr 0.044 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 947 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing