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Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose and AMP bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 23% PEG 4000, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D-ribose form. Subunit B contains AMP and ADP-ribose in the active site and were refined with grouped occupancies. plate Liu-S-102, F8. Puck: PSL-1011, Cryo: 10% extra PEG 4000 added to the drop.
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.826 α = 90 b = 92.659 β = 91.68 c = 57.716 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 EIGER2 XE 9M 2024-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 1.3 36.58 97.7 0.056 0.061 0.023 0.999 14.3 6.4 100227
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 80 0.692 0.793 0.377 0.695 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.3 36.58 1.34 100180 4954 97.69 0.1378 0.1365 0.1467 0.1635 0.1718
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.751 f_angle_d 1.019 f_chiral_restr 0.078 f_plane_restr 0.011 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3229 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing