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Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD
Crystal Properties Matthews coefficient Solvent content 4.06 69.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.744 α = 90 b = 95.997 β = 90 c = 57.725 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 EIGER X 16M 2017-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
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 2.082 47.999 61.9 0.045 0.051 0.019 1 20.7 7.4 8432
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 2.082 2.152 33.5 0.461 0.496 0.175 0.966 4.1 7.9
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 FREE R-VALUE 4IR5 2.082 47.998 1.34 8418 446 61.84 0.212 0.2101 0.2111 0.2459 0.2484 31.8278
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 13.802 f_angle_d 0.572 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 940 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction STARANISO data scaling