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Crystal structure of NUDT5 bound to dNUDT5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298.15 0.2 M sodium acetate, 0.1 M Tris pH 8.5, and 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 1.99 38.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.571 α = 90 b = 40.209 β = 121.921 c = 99.96 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 EIGER2 XE 16M 2022-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 42.43 99.9 0.997 0.504 6.8 30533 28.74
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 1.9 1.93 0.275
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 42.42 1.33 29977 1457 98.2 0.214 0.2125 0.2125 0.2422 0.2404 46.11
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 6.4314 f_angle_d 0.5417 f_chiral_restr 0.0438 f_plane_restr 0.005 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3004 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 73
Software Software Software Name Purpose xia2 data scaling PHENIX refinement