☰ Navigation Tabs
Structure of NUDT15 R139H 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 0.1 M MMT pH 5.0, 25.4% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.21 44.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.276 α = 100.08 b = 60.215 β = 104.102 c = 69.303 γ = 90.25
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 40.59 96.8 0.998 11.5 3.6 81339
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 0.976
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 40.59 81322 2415 96.797 0.186 0.1849 0.195 0.2201 0.2289 30.762
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] 5.219 -0.246 -0.763 -3.065 -1.316 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.065 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 13.347 r_dihedral_angle_1_deg 7.201 r_lrange_it 6.939 r_lrange_other 6.928 r_scangle_it 5.393 r_scangle_other 5.393 r_mcangle_it 3.741 r_mcangle_other 3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.065 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 13.347 r_dihedral_angle_1_deg 7.201 r_lrange_it 6.939 r_lrange_other 6.928 r_scangle_it 5.393 r_scangle_other 5.393 r_mcangle_it 3.741 r_mcangle_other 3.74 r_scbond_it 3.606 r_scbond_other 3.605 r_mcbond_it 2.693 r_mcbond_other 2.687 r_angle_refined_deg 1.703 r_angle_other_deg 1.383 r_symmetry_nbd_refined 0.289 r_nbd_other 0.212 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_other 0.112 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.013 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 5046 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing