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Neutron crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 8-oxo-dGTP
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 sodium citrate, cacodylate, NaCl
Crystal Properties Matthews coefficient Solvent content 1.9 35.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.85 α = 90 b = 48.16 β = 90 c = 124.1 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 PILATUS 2M 2018-12-16 M SINGLE WAVELENGTH 2 1 neutron 100 IMAGE PLATE BIODIFF 2018-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A 2 NUCLEAR REACTOR FRM II BEAMLINE BIODIFF 3.1 FRM II BIODIFF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.4 32.08 97.8 0.042 26.7 6.6 53822 10.02 2 1.7 38.05 83.7 0.142 5.5 2.6 26291 10.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 0.203 2 1.7 1.75 0.387
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS 1.4 32.08 1.35 53817 2688 97.8 0.1752 0.1741 0.1745 0.1969 0.1972 20.43 NEUTRON DIFFRACTION FOURIER SYNTHESIS 1.7 38.05 26267 1318 83.46 0.2153 0.2397
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 18.1876 f_angle_d 1.573 f_chiral_restr 0.0943 f_bond_d 0.0104 f_plane_restr 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2540 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement PHENIX phasing HKL-2000 data reduction XDS data scaling