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Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 Berkeley H6: 20% (w/v) PEG 1500, 12% (w/v) 1,6-hexanediol, 100 mM MES pH5.5, 100 mM CaCl2. 2mM CoA added prior to crystallization but not observed in the electron density. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. Plate: 13151, well H6 drop 3, Puck: PSL-1415, Cryo: 80% Berkeley H6 + 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.905 α = 90 b = 48.733 β = 95.42 c = 65.73 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 2022-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 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 1.15 48.73 98.6 0.043 0.046 0.018 0.999 15.9 6.2 68101
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 1.15 1.17 81.9 0.637 0.738 0.362 0.774 3.9
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 1.15 30.77 1 68044 3343 98.55 0.1414 0.1401 0.1511 0.1663 0.1766
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 13.578 f_angle_d 0.914 f_chiral_restr 0.07 f_plane_restr 0.012 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1552 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing