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Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with Ibrutinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Apo structure solved
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Tris, PEG4K, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.71 α = 80.652 b = 59.2 β = 82.958 c = 79.431 γ = 77.028
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 PILATUS 6M 2019-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.02 49.56 96.87 0.05739 0.07063 0.04047 0.994 7.35 2.8 53078
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.092 0.8753 0.243
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 FREE R-VALUE 2.02 49.557 52925 2657 96.943 0.224 0.2207 0.2298 0.289 0.293 45.269
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] 2.076 1.454 2.016 -0.918 1.351 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.934 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_6_deg 13.677 r_lrange_other 9.312 r_lrange_it 9.31 r_dihedral_angle_1_deg 7.878 r_scangle_it 7.107 r_scangle_other 7.106 r_mcangle_it 6.472 r_mcangle_other 6.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.934 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_6_deg 13.677 r_lrange_other 9.312 r_lrange_it 9.31 r_dihedral_angle_1_deg 7.878 r_scangle_it 7.107 r_scangle_other 7.106 r_mcangle_it 6.472 r_mcangle_other 6.471 r_scbond_it 4.837 r_scbond_other 4.836 r_mcbond_it 4.603 r_mcbond_other 4.601 r_dihedral_angle_other_2_deg 1.89 r_angle_refined_deg 1.773 r_angle_other_deg 0.584 r_nbd_refined 0.22 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.18 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.12 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.061 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5894 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data scaling