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Complex between MTH1 and compound 16 (a 4-amino-7-azaindole derivative)
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, HANGING DROP 3.6 293 23% PEG 6000, 0.28M lithium sulfate, 0.1M sodium acetate pH 3.6
Crystal Properties Matthews coefficient Solvent content 2.28 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.42 α = 90 b = 67.08 β = 90 c = 83.41 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 PILATUS 6M-F Toroidal mirror 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972957 ESRF ID23-1
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 1.84 48.4 99.7 0.148 0.063 0.996 3.9 6.5 29541
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.9 99.3 1.877 0.832 0.518 0.5 6
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 3Q93 1.84 48.4 28037 1443 99.57 0.22305 0.22114 0.23 0.25872 0.27 RANDOM 30.885
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] 0.32 0.31 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.696 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_4_deg 12.571 r_dihedral_angle_1_deg 6.635 r_long_range_B_refined 5.839 r_long_range_B_other 5.839 r_angle_refined_deg 1.559 r_scangle_other 0.948 r_angle_other_deg 0.889 r_scbond_it 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.696 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_4_deg 12.571 r_dihedral_angle_1_deg 6.635 r_long_range_B_refined 5.839 r_long_range_B_other 5.839 r_angle_refined_deg 1.559 r_scangle_other 0.948 r_angle_other_deg 0.889 r_scbond_it 0.694 r_scbond_other 0.694 r_mcangle_it 0.432 r_mcangle_other 0.432 r_mcbond_it 0.253 r_mcbond_other 0.253 r_chiral_restr 0.087 r_bond_refined_d 0.012 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 2540 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing