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Crystal structure of human MTH1 in complex with fragment inhibitor 8-(methylsulfanyl)-7H-purin-6-amine
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 5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (30% (w/v) PEG6000, 0.1 mol/L Sodium Acetate pH 3.7 and 0.2 mol/L LiSO4 in a 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.902 α = 90 b = 67.842 β = 90 c = 82.131 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 PILATUS3 2M 2015-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 48.4 99.9 0.234 0.991 8.1 6.3 17597
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 2.007 0.545 2 6.5
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 2.2 48.4 16625 927 99.86 0.21275 0.21036 0.2202 0.2539 0.2609 RANDOM 36.83
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] -1.35 -1.04 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 15.805 r_dihedral_angle_3_deg 15.507 r_long_range_B_refined 8.677 r_long_range_B_other 8.676 r_dihedral_angle_1_deg 7.036 r_scangle_other 5.961 r_mcangle_it 4.695 r_mcangle_other 4.694 r_scbond_it 3.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 15.805 r_dihedral_angle_3_deg 15.507 r_long_range_B_refined 8.677 r_long_range_B_other 8.676 r_dihedral_angle_1_deg 7.036 r_scangle_other 5.961 r_mcangle_it 4.695 r_mcangle_other 4.694 r_scbond_it 3.809 r_scbond_other 3.68 r_mcbond_it 2.887 r_mcbond_other 2.885 r_angle_refined_deg 1.541 r_angle_other_deg 0.891 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2508 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing