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Structure of NUDT15 V18_V19insGV 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 0.09 M SPG pH 5.0, 22.25% PEG 1500, 0.01 M sodium phosphate, 2.75% 1,2 propandiol, 1.0% glycerol
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.431 α = 90 b = 45.71 β = 115.103 c = 66.339 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 PILATUS3 S 6M 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96852 Diamond I24
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 1.45 60.073 100 1 24.7 31.5 61265
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 1.45 1.47 0.861
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LPG 1.45 60.073 61083 1996 99.732 0.168 0.1671 0.1973 0.1922 20.958
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] -1.357 -0.433 1.173 0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.41 r_dihedral_angle_4_deg 14.044 r_dihedral_angle_3_deg 11.666 r_dihedral_angle_1_deg 7.422 r_lrange_it 6.389 r_lrange_other 6.154 r_scangle_it 4.592 r_scangle_other 4.591 r_scbond_it 2.926 r_scbond_other 2.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.41 r_dihedral_angle_4_deg 14.044 r_dihedral_angle_3_deg 11.666 r_dihedral_angle_1_deg 7.422 r_lrange_it 6.389 r_lrange_other 6.154 r_scangle_it 4.592 r_scangle_other 4.591 r_scbond_it 2.926 r_scbond_other 2.925 r_mcangle_it 2.714 r_mcangle_other 2.714 r_mcbond_it 1.881 r_mcbond_other 1.881 r_angle_refined_deg 1.863 r_angle_other_deg 1.472 r_nbd_other 0.276 r_nbd_refined 0.246 r_symmetry_nbd_refined 0.244 r_xyhbond_nbd_other 0.215 r_xyhbond_nbd_refined 0.206 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.175 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2510 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing