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Structure of NUDT15 V18I 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, 20% PEG 500 MME, 20% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.1 41.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.538 α = 90 b = 34.624 β = 148.548 c = 75.17 γ = 90
Symmetry Space Group C 1 2 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 2019-11-21 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 1.5 39.22 100 0.994 8.6 6.6 25129
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 1.5 1.53 0.949
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 1.5 39.22 25125 1247 99.96 0.182 0.1803 0.1805 0.2127 0.2131 39.688
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] -1.893 0.333 -4.985 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_3_deg 13.845 r_dihedral_angle_4_deg 13.414 r_lrange_it 7.821 r_lrange_other 7.793 r_dihedral_angle_1_deg 6.976 r_scangle_it 6.509 r_scangle_other 6.505 r_scbond_it 4.409 r_scbond_other 4.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.117 r_dihedral_angle_3_deg 13.845 r_dihedral_angle_4_deg 13.414 r_lrange_it 7.821 r_lrange_other 7.793 r_dihedral_angle_1_deg 6.976 r_scangle_it 6.509 r_scangle_other 6.505 r_scbond_it 4.409 r_scbond_other 4.406 r_mcangle_it 4.147 r_mcangle_other 4.144 r_mcbond_it 3.068 r_mcbond_other 3.048 r_angle_refined_deg 1.739 r_angle_other_deg 1.406 r_nbd_other 0.301 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.183 r_symmetry_nbd_refined 0.175 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1248 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing