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Crystal structure of human MTH1 in complex with O6-methyl-dGMP
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 3.7 293 26% w/v PEG6000, 0.1 M Sodium acetate trihydrate pH 3.7, 0.2 M LiSO4, 3 mM O6-methyl-2'-dGTP, 2 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.581 α = 90 b = 67.237 β = 90 c = 79.025 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 CCD MARMOSAIC 225 mm CCD 2011-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91801 BESSY 14.1
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 1.8 47.57 98.9 0.085 0.999 13.7 4.5 29598
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 1.8 1.84 97.7 0.823 0.756 2.1 4.5
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 1.8 47.57 28070 1487 98.49 0.19861 0.19612 0.2074 0.24688 0.2536 RANDOM 24.366
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] -0.96 -1.11 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.395 r_dihedral_angle_3_deg 12.44 r_dihedral_angle_4_deg 10.854 r_dihedral_angle_1_deg 6.525 r_long_range_B_refined 5.26 r_long_range_B_other 5.192 r_angle_refined_deg 1.326 r_angle_other_deg 0.822 r_scangle_other 0.485 r_mcangle_it 0.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.395 r_dihedral_angle_3_deg 12.44 r_dihedral_angle_4_deg 10.854 r_dihedral_angle_1_deg 6.525 r_long_range_B_refined 5.26 r_long_range_B_other 5.192 r_angle_refined_deg 1.326 r_angle_other_deg 0.822 r_scangle_other 0.485 r_mcangle_it 0.357 r_mcangle_other 0.357 r_scbond_it 0.313 r_scbond_other 0.313 r_mcbond_it 0.208 r_mcbond_other 0.207 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 2552 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing