☰ Navigation Tabs
Crystal structure of 5-phosphomethyl-2'-deoxyuridine (5-PmdU) glycinyltransferase gp46/PUGT from Pseudomonads phage PaMx11 in complex with dsDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Z2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) PEG 8,000, 0.1M MES/Sodium hydroxide pH 6.0, 0.2M Calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.787 α = 90 b = 92.032 β = 90 c = 167.644 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97915 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 30 99.9 0.154 0.16 0.043 0.999 12.7 13.5 40612 45.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 99.9 1.798 0.866 0.496 0.827 1.5 13.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8Z2M 2.3 29 1.33 40471 2038 99.78 0.2286 0.2262 0.2754 0.2534 57.86
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 21.0354 f_angle_d 1.0616 f_chiral_restr 0.0532 f_plane_restr 0.0169 f_bond_d 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4663 Nucleic Acid Atoms 502 Solvent Atoms 43 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing