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Crystal structure of human NSun6/tRNA/SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.8 289 0.1 M SPG, 26% (w/v) PEG 1500, 50 mM NaF
Crystal Properties Matthews coefficient Solvent content 4.13 70.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.236 α = 90 b = 170.262 β = 108.63 c = 76.883 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 2016-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 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 3.247 50 94.6 26.9 6.5 39477 53.82
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 5WWR 3.247 42.702 1.35 32578 1655 82.47 0.1949 0.1934 0.1983 0.2221 0.2245 53.9884
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 14.118 f_angle_d 0.783 f_chiral_restr 0.231 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7083 Nucleic Acid Atoms 3052 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