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Crystal structure of human NSun6/tRNA/SFG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WWQ 5WWQ, 2DU3 experimental model PDB 2DU3 5WWQ, 2DU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 289 0.1 M SPG, 25% (w/v) PEG 1500, 50 mM NaF
Crystal Properties Matthews coefficient Solvent content 4.18 70.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.908 α = 90 b = 170.478 β = 108.55 c = 76.999 γ = 90
Symmetry Space Group C 1 2 1
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 S 6M 2016-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97776 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.096 50 98.2 19.7 6.7 45890 61.73
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 5WWQ, 2DU3 3.096 42.892 1.35 36230 1793 78.69 0.1973 0.1953 0.1998 0.2352 0.235 55.2541
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 13.23 f_angle_d 0.593 f_chiral_restr 0.024 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7091 Nucleic Acid Atoms 3072 Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data scaling PHENIX refinement PDB_EXTRACT data extraction SCALEPACK data reduction PHASER phasing HKL data reduction SCALEPACK data scaling