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Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 0.2 M Sodium formate pH 7.2, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.07 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.74 α = 90.11 b = 62.6 β = 107.32 c = 75.658 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2023-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0722 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 47.4 89.2 0.069 0.097 0.068 0.975 7.2 2 31141
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 2.3 2.38 91.5 0.517 0.73 0.515 0.63 2
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 2.3 47.4 29591 1524 89.3 0.2507 0.24962 0.2551 0.27262 0.2825 RANDOM 43.369
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] -0.53 -0.1 -0.98 4.69 0.08 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.157 r_dihedral_angle_3_deg 17.832 r_long_range_B_refined 9.854 r_long_range_B_other 9.854 r_dihedral_angle_1_deg 7.963 r_scangle_other 6.322 r_mcangle_it 6.08 r_mcangle_other 6.079 r_scbond_it 3.864 r_scbond_other 3.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.157 r_dihedral_angle_3_deg 17.832 r_long_range_B_refined 9.854 r_long_range_B_other 9.854 r_dihedral_angle_1_deg 7.963 r_scangle_other 6.322 r_mcangle_it 6.08 r_mcangle_other 6.079 r_scbond_it 3.864 r_scbond_other 3.863 r_mcbond_it 3.819 r_mcbond_other 3.816 r_angle_refined_deg 1.713 r_angle_other_deg 1.259 r_chiral_restr 0.079 r_gen_planes_other 0.015 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4723 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing