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Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (AMP-PNP 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 E4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. 10 mM soak in AMP-PNP overnight. Plate: SS-Clover-3/17/23 wells H7, Puck: PSL-0116, Cryo: Direct
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.306 α = 90 b = 48.849 β = 96.61 c = 63.878 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 2023-06-15 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 1.5 63.45 100 0.036 0.039 0.015 1 19.4 6.8 31784
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 1.54 100 0.933 1.009 0.378 0.807 7
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 1.5 24.42 1.34 31746 1597 99.92 0.1934 0.192 0.1979 0.2204 0.2252
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 12.99 f_angle_d 0.523 f_chiral_restr 0.041 f_plane_restr 0.006 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1559 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing