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Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P21 Form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1 at 15 mg/mL, Tray: plate 12527 well A4 drop 1, Puck: PSL0809, Cryo: DIRECT; Electron density consistent with a benzoic acid molecule was observed and modeled. The source of this is unknown and it may have been acquired from the expression host
Crystal Properties Matthews coefficient Solvent content 2.13 42.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.35 α = 90 b = 70.5 β = 90.91 c = 66.84 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 2022-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97949 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 1.65 70.5 99.9 0.094 0.111 0.058 0.992 6.4 3.5 55090 16.81
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 1.65 1.69 99.6 0.355 0.418 0.218 0.896 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 8DOP 1.65 39.4 1.34 55008 2718 99.75 0.1807 0.1791 0.1857 0.2094 0.2155 26.6252
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3262 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 25
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction