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Crystal structure of mouse MTH1 mutant L116M with inhibitor TH588
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MZG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium nitrate, 34% (w/v) PEG 3350, 0.01 M copper (II) chloride dihydrate, 2 mM TCEP, 10 mM TH588, 6 mM MgCL2.
Crystal Properties Matthews coefficient Solvent content 2.9 57.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.673 α = 90 b = 142.088 β = 107.52 c = 58.75 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2017-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.4 47.4 99 0.271 0.981 5 3.9 35400
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 95.4 1.445 0.429 1.1 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5MZG 2.4 47.4 33560 1811 98.93 0.25118 0.24861 0.2516 0.29924 0.3013 RANDOM 27.34
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] -0.58 -0.3 1.25 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_3_deg 13.045 r_dihedral_angle_4_deg 12.711 r_dihedral_angle_1_deg 5.726 r_long_range_B_refined 2.644 r_long_range_B_other 2.644 r_mcangle_it 1.221 r_mcangle_other 1.221 r_angle_refined_deg 1.06 r_angle_other_deg 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_3_deg 13.045 r_dihedral_angle_4_deg 12.711 r_dihedral_angle_1_deg 5.726 r_long_range_B_refined 2.644 r_long_range_B_other 2.644 r_mcangle_it 1.221 r_mcangle_other 1.221 r_angle_refined_deg 1.06 r_angle_other_deg 0.805 r_scangle_other 0.796 r_mcbond_it 0.663 r_mcbond_other 0.663 r_scbond_it 0.429 r_scbond_other 0.429 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4966 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing