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Crystal structure of N6-methyladenosine RNA reader YTHDF2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 277 0.1M phosphate-citric pH 4.3, 0.2M Lithium Sulfate, 10% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.689 α = 90 b = 76.689 β = 90 c = 131.241 γ = 120
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 ADSC QUANTUM 315r 2014-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.12 50 100 0.113 0.119 0.037 9 10.5 24685 39.56
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 2.12 2.2 100 0.898 0.949 0.302 0.893 9.5 2447
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2YU6 2.121 38.344 1.35 24629 1261 99.51 0.1878 0.186 0.1879 0.2214 0.2217 47.1
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 13.463 f_angle_d 1.043 f_chiral_restr 0.084 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2478 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction