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Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L9L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol, 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1MBuffer System 3 (pH 8.5 Tris (base) and BICINE 1.0M each), 37.5% v/vPrecipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 4.3 71.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.29 α = 90 b = 165.19 β = 90 c = 108.69 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 CCD RIGAKU SATURN 944+ 2019-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 19.4 98.8 0.169 0.182 0.993 13.52 7.421 24881 27.984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 98.2 0.67 0.719 0.893 3.74 7.51
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 THROUGHOUT 7L9L 2.7 19.4 1.35 24876 996 99.12 0.1947 0.1931 0.1943 0.2319 0.2344 26.7621
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3651 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 188
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing