☰ Navigation Tabs
Crystal structure of human NSun6/tRNA
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 9.5 289 0.1 M SPG, 28% (w/v) PEG 1500, 50 mM NaF
Crystal Properties Matthews coefficient Solvent content 4.14 70.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.586 α = 90 b = 170.117 β = 108.19 c = 76.909 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 3.197 50 96.5 17.5 6.5 41488 54.59
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 3.197 42.76 1.36 33720 1665 81.22 0.1921 0.1904 0.1945 0.2233 0.2251 52.286
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 14.548 f_angle_d 0.622 f_chiral_restr 0.022 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7105 Nucleic Acid Atoms 3052 Solvent Atoms Heterogen Atoms
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