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Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.174 α = 90 b = 76.348 β = 90 c = 117.279 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 RAYONIX MX-225 2015-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.52 50 98.7 0.069 26.4 7.2 54317
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.55 0.575 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.52 50 51601 2642 98.6 0.1623 0.16093 0.1653 0.18931 0.192 RANDOM 20.342
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] -0.03 0.27 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_3_deg 12.66 r_dihedral_angle_4_deg 11.22 r_sphericity_bonded 9.388 r_dihedral_angle_1_deg 6.164 r_long_range_B_refined 4.023 r_mcangle_it 1.771 r_scbond_it 1.765 r_rigid_bond_restr 1.405 r_mcbond_it 1.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_3_deg 12.66 r_dihedral_angle_4_deg 11.22 r_sphericity_bonded 9.388 r_dihedral_angle_1_deg 6.164 r_long_range_B_refined 4.023 r_mcangle_it 1.771 r_scbond_it 1.765 r_rigid_bond_restr 1.405 r_mcbond_it 1.317 r_angle_refined_deg 1.299 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2458 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction MOLREP phasing