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Crystal structure of human Nudt15 (MTH2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291.2 Full length NUDT15 (20 mg/ml) was crystallized in the presence of alpha-Chymotrypsin (0.2 mg/ml) in 20 mM HEPES, pH 7.5, 300 mM NaCl, 10% Glycerol, and 1 mM TCEP. Sitting drop vapour diffusion experiments at 18 degrees C were performed, and NUDT15 was mixed with reservoir solution (30% PEG3350, 0.1 M Tris pH 8.5, and 0.05 M MgCl) in a 1:1 or 1:2 ratio.
Crystal Properties Matthews coefficient Solvent content 2.45 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.83 α = 90.07 b = 71.676 β = 90.04 c = 82.768 γ = 73.08
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 MARRESEARCH 2014-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 47.5 95.8 0.035 12.95 1.8 118878 28.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 93.9 0.747 1.4 1.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ZR0 1.799 47.598 1.96 118828 5943 95.74 0.194 0.1927 0.1939 0.22 0.2212 Random selection
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 21.607 f_angle_d 0.932 f_chiral_restr 0.04 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9894 Nucleic Acid Atoms Solvent Atoms 1111 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction XDS data scaling