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Crystal structure of YTHDF2 in complex with compound 20 (ZA801)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 Co-crystallized with ligand in 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, and 30%w/v PEG MME 5K
Crystal Properties Matthews coefficient Solvent content 1.91 35.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.796 α = 90 b = 46.295 β = 90 c = 72.845 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2024-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.675 39.072 99.9 0.998 10.2 10.5 17596 17.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.675 1.704 0.931
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.68 37.53 1.38 17583 871 99.81 0.1826 0.1817 0.1845 0.2006 0.2052 22.59
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.2538 f_angle_d 0.8134 f_chiral_restr 0.0555 f_plane_restr 0.0064 f_bond_d 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1168 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing