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The Crystal Structure of human MTH1 from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 277 0.1 M Citric Acid pH 4.0, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.81 32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.276 α = 90 b = 60.533 β = 90 c = 66.135 γ = 90
Symmetry Space Group P 2 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 6M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.521200 CLSI 08ID-1
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 1.55 44.653 99.4 0.076 28.3 11.1 21691
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 1.55 1.58 0.427
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3Q93 1.55 44.653 21655 1045 99.267 0.19 0.1885 0.203 0.215 0.226 16.016
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] 0.594 -0.516 -0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.526 r_dihedral_angle_3_deg 13.171 r_dihedral_angle_4_deg 10.806 r_dihedral_angle_1_deg 7.937 r_lrange_it 5.313 r_lrange_other 5.259 r_scangle_it 4.232 r_scangle_other 4.23 r_scbond_it 2.832 r_scbond_other 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.526 r_dihedral_angle_3_deg 13.171 r_dihedral_angle_4_deg 10.806 r_dihedral_angle_1_deg 7.937 r_lrange_it 5.313 r_lrange_other 5.259 r_scangle_it 4.232 r_scangle_other 4.23 r_scbond_it 2.832 r_scbond_other 2.83 r_mcangle_it 2.299 r_mcangle_other 2.298 r_angle_refined_deg 1.867 r_mcbond_it 1.603 r_mcbond_other 1.601 r_angle_other_deg 1.507 r_symmetry_nbd_refined 0.273 r_nbd_other 0.242 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1254 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing