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Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac 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 2.46 49.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.2 α = 90 b = 66.2 β = 90 c = 248.583 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 2019-04-08 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 2.1 50 91.1 0.118 9.9 10.9 34835
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 2.1 2.17 1.502 1.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 45.004 34022 1617 89.308 0.252 0.2496 0.2511 0.3009 0.2981 48.36
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] -0.002 -0.001 -0.002 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.639 r_dihedral_angle_3_deg 13.313 r_dihedral_angle_4_deg 11.81 r_dihedral_angle_1_deg 6.78 r_lrange_it 6.329 r_lrange_other 6.328 r_scangle_it 4.308 r_scangle_other 4.307 r_mcangle_it 4.302 r_mcangle_other 4.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.639 r_dihedral_angle_3_deg 13.313 r_dihedral_angle_4_deg 11.81 r_dihedral_angle_1_deg 6.78 r_lrange_it 6.329 r_lrange_other 6.328 r_scangle_it 4.308 r_scangle_other 4.307 r_mcangle_it 4.302 r_mcangle_other 4.301 r_mcbond_it 2.794 r_mcbond_other 2.794 r_scbond_it 2.704 r_scbond_other 2.703 r_angle_refined_deg 1.308 r_angle_other_deg 1.173 r_symmetry_nbd_refined 0.202 r_nbd_refined 0.19 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.151 r_symmetry_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4055 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing