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Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 30% (w/v) PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M Lithium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.616 α = 69.264 b = 46.364 β = 85.601 c = 57.704 γ = 90.015
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 2020-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 30 97.1 0.071 14.2 2.8 29797 19.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 0.276
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 6A6J 1.95 24.74 1.56 27986 1967 93.26 0.1903 0.1875 0.1891 0.2289 0.239 21.59
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 22.0919 f_angle_d 1.1021 f_chiral_restr 0.0628 f_bond_d 0.0073 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms 400 Solvent Atoms 348 Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing