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XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VNA 5VNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.6 α = 67.58 b = 47.44 β = 68.56 c = 58.45 γ = 69.02
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-11-30 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.83 42.41 96.1 0.138 0.195 0.138 0.956 7.4 1.8 34543
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 1.83 1.88 95 0.781 1.104 0.781 0.567 1.8 2543
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT 5VNA 1.83 42.45 32842 1701 96.04 0.2296 0.2286 0.2427 0.2476 0.2656 RANDOM 25.148
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] 2.49 1.11 1.12 0.48 1.11 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.473 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_4_deg 13.928 r_dihedral_angle_1_deg 8.033 r_mcangle_it 3.115 r_mcbond_it 2.061 r_mcbond_other 2.06 r_angle_refined_deg 1.599 r_angle_other_deg 1.283 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.473 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_4_deg 13.928 r_dihedral_angle_1_deg 8.033 r_mcangle_it 3.115 r_mcbond_it 2.061 r_mcbond_other 2.06 r_angle_refined_deg 1.599 r_angle_other_deg 1.283 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2191 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing