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Structure of NUDT15 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 0.1 M Tris pH 8.0, 0.2 M sodium acetate, 38% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.602 α = 90 b = 45.641 β = 115.998 c = 67.023 γ = 90
Symmetry Space Group P 1 21 1
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 2019-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.91840 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 60.24 100 0.999 15.1 6.8 45919
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 0.862
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 60.24 45895 2245 99.963 0.168 0.1669 0.1805 0.1962 0.2059 24.514
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] -1.506 -0.266 0.832 0.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.511 r_dihedral_angle_4_deg 16.833 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_1_deg 7.474 r_lrange_it 6.889 r_lrange_other 6.648 r_scangle_it 5.145 r_scangle_other 5.143 r_scbond_it 3.31 r_scbond_other 3.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.511 r_dihedral_angle_4_deg 16.833 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_1_deg 7.474 r_lrange_it 6.889 r_lrange_other 6.648 r_scangle_it 5.145 r_scangle_other 5.143 r_scbond_it 3.31 r_scbond_other 3.309 r_mcangle_it 3.22 r_mcangle_other 3.219 r_mcbond_it 2.24 r_mcbond_other 2.239 r_angle_refined_deg 1.827 r_angle_other_deg 1.455 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.191 r_xyhbond_nbd_refined 0.184 r_nbd_other 0.183 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.173 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 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 2512 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing