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Crystal structure of human GCN5 histone acetyltransferase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TRL 5TRL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1 M Succinic acid pH 7.0, 0.1 M HEPES pH 7, and 1% w/v PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.889 α = 90 b = 137.889 β = 90 c = 154.875 γ = 90
Symmetry Space Group I 4 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 80 CCD MARMOSAIC 300 mm CCD 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.37 50 100 0.083 0.086 0.024 9.4 12.6 30628 44.55
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 2.37 2.41 100 0.77 0.807 0.239 0.864 11.4
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 5TRL 2.37 43.6 1.35 30528 1999 99.55 0.2075 0.2051 0.2056 0.2424 0.2435 47.24
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 5.4382 f_angle_d 0.5312 f_chiral_restr 0.0455 f_plane_restr 0.0032 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3993 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 159
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing