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Crystal structure of MTH1 in complex with compound 32
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 3.5 277 23% (w/v) PEG 6k, 200 mM lithium sulfate, 100 mM sodium acetate pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.21 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.607 α = 90 b = 67.835 β = 90 c = 79.061 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 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.59 51.48 100 0.17 0.05 0.999 10 13.4 43865
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 1.59 1.63 100 0.918 0.587 1.1
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 1.59 51.48 43523 2194 99.284 0.214 0.2116 0.2229 0.254 0.2585 17.759
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] -1.08 -0.354 1.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.639 r_dihedral_angle_3_deg 14.719 r_dihedral_angle_4_deg 10.9 r_dihedral_angle_1_deg 8.339 r_lrange_it 5.984 r_lrange_other 5.876 r_scangle_it 4.086 r_scangle_other 4.025 r_mcangle_it 2.629 r_mcangle_other 2.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.639 r_dihedral_angle_3_deg 14.719 r_dihedral_angle_4_deg 10.9 r_dihedral_angle_1_deg 8.339 r_lrange_it 5.984 r_lrange_other 5.876 r_scangle_it 4.086 r_scangle_other 4.025 r_mcangle_it 2.629 r_mcangle_other 2.629 r_scbond_it 2.616 r_scbond_other 2.566 r_mcbond_it 1.679 r_mcbond_other 1.678 r_angle_refined_deg 1.371 r_angle_other_deg 1.327 r_symmetry_nbd_refined 0.272 r_symmetry_nbd_other 0.2 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_other 0.155 r_nbd_other 0.149 r_ncsr_local_group_1 0.131 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2508 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing