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Crystal structure of PHD finger-linker-bromodomain Y17E mutant from human BPTF in the H3(1-9)K4ME2 bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 BPTF Y17E PHD finger-linker-bromodomain (16.5 mg/ml, 20 mM Tris-HCl pH 7.5, 50 mM KCl) was pre-incubated with three-fold molar excess of H3(1-9)K4me2 peptide in the presence of 5 mM MgCl2 for about 30 min on ice. Drops were made by mixing 2 l each of the complex with the reservoir solution: 8.5% isopropanol, 0.085 M Hepes-Na, pH 7.5, 17% PEG 4000, 15% Glycerol. A 0.3 l of 1 M KCl was then added to the drops as additive., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.249 α = 90 b = 64.381 β = 90 c = 85.558 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 2006-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.45 20 100 0.07 0.07 39.1 10.3 38245 38245 -3 -3 12.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 100 0.49 0.49 5.6 10.3 3744
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FSA 1.45 20 38232 38183 1914 99.9 0.189 0.1912 0.192 0.1955 random 16.8
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 c_angle_deg 1.42 c_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1430 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 12
Software Software Software Name Purpose ADSC data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling