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Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212
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 8 290 0.1 M Tris pH 8.0, 3.2 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.76 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.749 α = 90 b = 33.135 β = 90 c = 33.693 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 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 1.76 50 99.9 0.072 35.3 12.5 8891 17.23
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 1.76 1.79 0.104
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 1.76 33.69 1.54 8859 1591 99.84 0.1487 0.1458 0.1461 0.1757 0.1765 18.32
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 26.9357 f_angle_d 1.1045 f_chiral_restr 0.0513 f_bond_d 0.0065 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 699 Nucleic Acid Atoms 120 Solvent Atoms 125 Heterogen Atoms 10
Software Software Software Name Purpose Coot model building PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing