☰ Navigation Tabs
Structure of rat GLD-2 (Terminal nucleotidyltransferase 2, TENT2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JNB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.15 22.4% PEG 3350, 100 mM Tris-HCl pH 8.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.96 α = 90 b = 40.72 β = 100.204 c = 105 γ = 90
Symmetry Space Group P 1 21 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 2017-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.977760 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.49 47.2 99.11 0.05 0.999 21.5 6.5 44966 60.3345537444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4956881144 2.58 0.524 0.914
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 5JNB 2.4956881144 47.1978941949 1.37375040396 44966 2320 99.1598121155 0.206856945188 0.204826722881 0.214 0.242530638455 0.2529 82.5432496443
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 20.2492974018 f_angle_d 1.21293040556 f_chiral_restr 0.0706822640005 f_bond_d 0.0102089982048 f_plane_restr 0.00808731702822
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5235 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MrBUMP phasing