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Crystal structure of mouse MTH1 in complex with TH588
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M potassium thiocyanate and 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.006 α = 90 b = 67.708 β = 90 c = 123.133 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 4M 2015-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 1.85 61.57 100 0.071 16.3 6.5 29434
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 1.85 1.89 100 0.617 3 6.3 1775
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 3ZR1 1.85 45.6 27865 1492 99.89 0.18146 0.17953 0.1919 0.2187 0.2247 RANDOM 29.668
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] 2.34 -0.1 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.785 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 6.999 r_long_range_B_refined 6.798 r_long_range_B_other 6.757 r_scangle_other 4.846 r_scbond_it 3.146 r_scbond_other 3.032 r_mcangle_it 2.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.785 r_dihedral_angle_4_deg 18.326 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 6.999 r_long_range_B_refined 6.798 r_long_range_B_other 6.757 r_scangle_other 4.846 r_scbond_it 3.146 r_scbond_other 3.032 r_mcangle_it 2.996 r_mcangle_other 2.996 r_mcbond_it 2.096 r_mcbond_other 2.012 r_angle_refined_deg 1.503 r_angle_other_deg 0.741 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 2498 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing