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Complex between MTH1 and compound 7 (a 7-azaindole-2-amide 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, SITTING DROP 3.6 277 26% PEG6000, 0.1M Na-acetate pH 3.6, 0.22M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.29 46.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.38 α = 90 b = 67.27 β = 90 c = 82.29 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 2014-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97626 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 1.9 48.68 98.8 0.164 0.171 0.047 0.998 12.4 13.1 26731
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 1.9 1.97 98.2 1.732 1.804 0.498 0.597 1.6 12.7
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 1.9 48.68 25354 1331 98.57 0.19663 0.19409 0.2042 0.24483 0.2482 RANDOM 28.308
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] -0.75 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.827 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_4_deg 8.733 r_dihedral_angle_1_deg 6.757 r_long_range_B_refined 6.664 r_long_range_B_other 6.645 r_scangle_other 4.641 r_scbond_it 2.972 r_scbond_other 2.863 r_mcangle_other 2.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.827 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_4_deg 8.733 r_dihedral_angle_1_deg 6.757 r_long_range_B_refined 6.664 r_long_range_B_other 6.645 r_scangle_other 4.641 r_scbond_it 2.972 r_scbond_other 2.863 r_mcangle_other 2.738 r_mcangle_it 2.737 r_mcbond_it 1.822 r_mcbond_other 1.82 r_angle_refined_deg 1.519 r_angle_other_deg 0.853 r_chiral_restr 0.09 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 2512 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing