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Crystal structure of AF9 YEATS domain in complex with dicrotonylated at K1007 and K1014 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 Lithium nitrate pH 7.1, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.66 66.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.364 α = 90 b = 49.021 β = 113.64 c = 78.133 γ = 90
Symmetry Space Group C 1 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 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 2.1 45.97 94.2 0.056 0.066 0.034 0.999 8.7 3.6 27648
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 2.1 2.16 99.6 0.632 0.754 0.407 0.867 3.3
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 2.1 45.97 25539 1318 91.47 0.20529 0.20307 0.213 0.24748 0.2515 RANDOM 48.129
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] -3.71 -0.37 5.99 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.84 r_long_range_B_other 12.899 r_long_range_B_refined 12.879 r_scangle_other 10.165 r_dihedral_angle_2_deg 7.645 r_dihedral_angle_1_deg 7.516 r_mcangle_it 7.093 r_mcangle_other 7.092 r_scbond_it 7.085 r_scbond_other 7.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.84 r_long_range_B_other 12.899 r_long_range_B_refined 12.879 r_scangle_other 10.165 r_dihedral_angle_2_deg 7.645 r_dihedral_angle_1_deg 7.516 r_mcangle_it 7.093 r_mcangle_other 7.092 r_scbond_it 7.085 r_scbond_other 7.082 r_mcbond_it 5.318 r_mcbond_other 5.28 r_angle_refined_deg 1.649 r_angle_other_deg 0.626 r_chiral_restr 0.072 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 2422 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing