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Human NUDT5 in complex with MRK-952
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished NUDT5 structure solved in the lab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Reservoir: 33% PEG 400, 0.2 M magnesium chloride, and 0.1 M tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.245 α = 78.789 b = 59.679 β = 81.715 c = 81.171 γ = 76.034
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 2021-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 28.41 98.4 0.051 9.2 3.2 29822 33.048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 97.9 0.225 2.9 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.5 28.41 29822 1433 98.439 0.181 0.178 0.1835 0.2453 0.2446 39.036
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] 2.431 0.788 0.886 -0.257 0.678 -1.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.43 r_dihedral_angle_6_deg 12.941 r_dihedral_angle_2_deg 7.804 r_dihedral_angle_1_deg 6.731 r_lrange_it 4.989 r_lrange_other 4.969 r_mcangle_it 2.856 r_mcangle_other 2.855 r_scangle_it 2.825 r_scangle_other 2.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.43 r_dihedral_angle_6_deg 12.941 r_dihedral_angle_2_deg 7.804 r_dihedral_angle_1_deg 6.731 r_lrange_it 4.989 r_lrange_other 4.969 r_mcangle_it 2.856 r_mcangle_other 2.855 r_scangle_it 2.825 r_scangle_other 2.825 r_mcbond_it 1.663 r_mcbond_other 1.662 r_scbond_it 1.625 r_scbond_other 1.625 r_angle_refined_deg 1.226 r_angle_other_deg 0.289 r_chiral_restr 0.232 r_nbd_refined 0.186 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.166 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6062 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing REFMAC refinement