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Crystal structure of MTH1 in complex with compound 31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3 277 29.5% (w/v) PEG 6k, 200 mM lithium sulfate, 100 mM sodium acetate pH 3.0
Crystal Properties Matthews coefficient Solvent content 2.01 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.806 α = 90 b = 66.068 β = 90 c = 36.585 γ = 90
Symmetry Space Group P 21 21 2
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 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.13 44.34 98.9 0.06 0.02 0.999 17.6 12.3 54483
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.17 89.1 0.68 0.604 1.5 9.2
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 5ANV 1.13 44.338 54428 2693 98.865 0.153 0.1514 0.1521 0.1831 0.1837 18.354
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] -0.357 -0.131 0.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.459 r_dihedral_angle_4_deg 16.377 r_dihedral_angle_3_deg 12.915 r_rigid_bond_restr 9.099 r_dihedral_angle_1_deg 7.893 r_scangle_it 4.942 r_mcbond_it 4.778 r_mcbond_other 4.777 r_scangle_other 4.765 r_scbond_it 4.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.459 r_dihedral_angle_4_deg 16.377 r_dihedral_angle_3_deg 12.915 r_rigid_bond_restr 9.099 r_dihedral_angle_1_deg 7.893 r_scangle_it 4.942 r_mcbond_it 4.778 r_mcbond_other 4.777 r_scangle_other 4.765 r_scbond_it 4.634 r_scbond_other 4.565 r_lrange_it 4.473 r_lrange_other 4.425 r_mcangle_it 4.371 r_mcangle_other 4.369 r_angle_refined_deg 2.049 r_angle_other_deg 1.668 r_symmetry_nbd_refined 0.319 r_symmetry_xyhbond_nbd_other 0.232 r_nbd_other 0.229 r_nbd_refined 0.228 r_symmetry_nbd_other 0.211 r_xyhbond_nbd_refined 0.206 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.137 r_chiral_restr 0.131 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_bond_other_d 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1254 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing