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Structure of NUDT15 R139C Mutant in complex with TH7755
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.12 M Monosaccharide mix (Morpheus Screen) 0.1 M Imidazole/MES pH 6,5, 12.5% MPD, 12.5% PEG 1000, 12.5 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.91 α = 91.582 b = 43.803 β = 106.74 c = 60.457 γ = 113.478
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 16M 2019-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97622 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 35.37 96.6 0.997 16.2 3.6 39574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.985
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 5LPG 1.6 35.37 39573 1981 96.595 0.161 0.1597 0.1726 0.1843 0.1926 21.914
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] 0.797 0.265 -0.433 0.964 -0.403 -1.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.615 r_dihedral_angle_3_deg 13.002 r_dihedral_angle_4_deg 9.987 r_dihedral_angle_1_deg 7.111 r_lrange_it 6.506 r_lrange_other 6.397 r_scangle_it 5.196 r_scangle_other 5.194 r_scbond_it 3.405 r_scbond_other 3.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.615 r_dihedral_angle_3_deg 13.002 r_dihedral_angle_4_deg 9.987 r_dihedral_angle_1_deg 7.111 r_lrange_it 6.506 r_lrange_other 6.397 r_scangle_it 5.196 r_scangle_other 5.194 r_scbond_it 3.405 r_scbond_other 3.404 r_mcangle_it 3.023 r_mcangle_other 3.023 r_mcbond_it 2.127 r_mcbond_other 2.123 r_angle_refined_deg 1.886 r_angle_other_deg 1.497 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_refined 0.207 r_nbd_other 0.199 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.12 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.072 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2472 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing