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Complex between MTH1 and compound 29 (a 4-amino-2,7-diazaindole derivative)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 22% PEG4K, 0.24M AmSO4, 12.5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.466 α = 90 b = 66.626 β = 90 c = 83.076 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 2015-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97295 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.55 51.98 99.1 0.069 0.079 0.037 0.998 12.8 4.4 48090
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 98.9 0.904 1.028 0.481 0.555 1.8
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 5nhy 1.55 51.98 45708 2326 98.84 0.17118 0.16941 0.182 0.20546 0.2154 RANDOM 18.783
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] -0.95 -0.24 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.895 r_sphericity_free 24.263 r_rigid_bond_restr 13.03 r_dihedral_angle_3_deg 12.316 r_dihedral_angle_4_deg 9.821 r_sphericity_bonded 8.215 r_dihedral_angle_1_deg 6.437 r_angle_other_deg 3.617 r_long_range_B_refined 3.214 r_long_range_B_other 3.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.895 r_sphericity_free 24.263 r_rigid_bond_restr 13.03 r_dihedral_angle_3_deg 12.316 r_dihedral_angle_4_deg 9.821 r_sphericity_bonded 8.215 r_dihedral_angle_1_deg 6.437 r_angle_other_deg 3.617 r_long_range_B_refined 3.214 r_long_range_B_other 3.171 r_scangle_other 2.389 r_mcangle_other 2.207 r_mcangle_it 2.206 r_scbond_it 1.913 r_scbond_other 1.883 r_mcbond_it 1.633 r_mcbond_other 1.631 r_angle_refined_deg 1.359 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2530 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing