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Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (Sulfate bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Crystal Screen D3: 2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% (v/v) PEG 400. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. plate 13976 well D3 drop 2, Puck: PSL-2011, Cryo: 2.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.1 41.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.801 α = 90 b = 49.228 β = 90 c = 94.916 γ = 90
Symmetry Space Group P 21 21 21
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 2024-08-03 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 1.5 94.92 100 0.071 0.076 0.026 0.999 15.8 8.2 32947
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 1.5 1.54 99.9 1.208 1.284 0.431 0.691 8.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 47.46 1.33 32885 1588 99.93 0.1572 0.1551 0.1971 0.1979
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 12.992 f_angle_d 0.871 f_chiral_restr 0.051 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1637 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing