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Structure of mouse 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 7.4 291.15 23.6% PEG 3350, 80mM HEPEs pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.277 α = 87.381 b = 47.144 β = 88.056 c = 105.446 γ = 63.806
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2015-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.918003 SSRF BL17U1
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 2.7 42.28 88.3 0.091 0.977 11.2 2.6 17614 67.3048882299
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 83.5 0.835
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 2.70444053571 35.5139056296 1.95855275381 16025 925 80.3378954229 0.253956762327 0.252858949368 0.2549 0.270837041836 0.2716 91.2178284413
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 19.8660414836 f_angle_d 1.16217278923 f_chiral_restr 0.0816148036006 f_bond_d 0.00827865376677 f_plane_restr 0.00613584896334
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5292 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MrBUMP phasing