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Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac 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 Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.241 α = 90 b = 66.241 β = 90 c = 248.821 γ = 120
Symmetry Space Group P 32 2 1
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 MX225-HS 2018-08-02 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 2.15 50 100 0.093 14.5 11 35680
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 2.15 2.22 1.433
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 2.15 45 33750 1853 99.97 0.17359 0.16975 0.1747 0.24671 0.248 RANDOM 55.24
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] 0.41 0.21 0.41 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.183 r_dihedral_angle_4_deg 14.473 r_dihedral_angle_3_deg 11.912 r_long_range_B_refined 7.607 r_long_range_B_other 7.606 r_scangle_other 6.701 r_mcangle_other 5.983 r_mcangle_it 5.978 r_dihedral_angle_1_deg 5.971 r_scbond_it 5.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.183 r_dihedral_angle_4_deg 14.473 r_dihedral_angle_3_deg 11.912 r_long_range_B_refined 7.607 r_long_range_B_other 7.606 r_scangle_other 6.701 r_mcangle_other 5.983 r_mcangle_it 5.978 r_dihedral_angle_1_deg 5.971 r_scbond_it 5.595 r_scbond_other 5.595 r_mcbond_other 4.666 r_mcbond_it 4.659 r_rigid_bond_restr 1.508 r_angle_other_deg 1.179 r_angle_refined_deg 1.174 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4088 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing