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Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (CoA and ADP 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 6.5 291 Morpheus F4: 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 100 mM midazole/MES monohydrate (acid), pH 6.5, 20 mM D-Glucose; 20 mM D-Mannose; 20 mMD-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. Soak with 5mM ADP and 5 mM CoA in 18.75% v/v MPD; 18.75% PEG 1000; 18.75% w/v PEG 3350 for 10 days. Plate: Liu-S-118 Well G12 , Puck: PSL-0715, Cryo: 18.75% v/v MPD; 18.75% PEG 1000; 18.75% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.096 α = 90 b = 50.551 β = 115.22 c = 70.595 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 2024-04-13 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 2.35 39.64 99.9 0.088 0.096 0.037 0.999 11.8 6.9 18892
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 2.35 2.43 100 1.154 1.248 0.471 0.787 6.9
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 2.35 39.64 1.35 18851 948 99.77 0.234 0.2313 0.2346 0.2831 0.2812
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 20.69 f_angle_d 0.636 f_chiral_restr 0.041 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3034 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 102
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing