☰ Navigation Tabs
Human NUDT5 with ibrutinib derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NUDT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.2 M ammonium acetate,
0.1 M citrate pH 5.5,
30 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.88 57.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.605 α = 90 b = 60.605 β = 90 c = 502.608 γ = 120
Symmetry Space Group P 61 2 2
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 4M 2022-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 2.288 83.768 85.8 0.335 10.3 35.1 9387
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 2.288 2.646 2.541 1.8
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 2.288 83.768 9387 450 35.535 0.229 0.2255 0.2263 0.2948 0.301 44.38
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] 0.518 0.259 0.518 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.396 r_dihedral_angle_3_deg 17.443 r_dihedral_angle_4_deg 16.452 r_lrange_it 7.152 r_lrange_other 7.148 r_dihedral_angle_1_deg 7.027 r_mcangle_it 4.602 r_mcangle_other 4.601 r_scangle_it 4.014 r_scangle_other 4.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.396 r_dihedral_angle_3_deg 17.443 r_dihedral_angle_4_deg 16.452 r_lrange_it 7.152 r_lrange_other 7.148 r_dihedral_angle_1_deg 7.027 r_mcangle_it 4.602 r_mcangle_other 4.601 r_scangle_it 4.014 r_scangle_other 4.013 r_mcbond_it 2.722 r_mcbond_other 2.716 r_scbond_it 2.337 r_scbond_other 2.337 r_angle_refined_deg 1.374 r_angle_other_deg 1.14 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.2 r_nbd_other 0.195 r_xyhbond_nbd_refined 0.182 r_symmetry_nbd_other 0.18 r_symmetry_nbd_refined 0.173 r_nbtor_refined 0.155 r_ncsr_local_group_1 0.122 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.045 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_symmetry_xyhbond_nbd_other 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 2922 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing