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Crystal structure of okaE in complex with a-ketoglutarate and okaramine A at 2.5 angstroms resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A2Z5U507-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M imidazole, 0.1M MES monohydrate, pH=6.5, 20% PEG 500 MME, 10% PEG 20000, 0.02M D-Glucose, 0.02M D-Mannose, 0.02M DGalactose, 0.02M L-Fucose, 0.02M D-Xylose,
0.02M N-Acetyl-D-Glucosamine
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.121 α = 90 b = 107.661 β = 90 c = 134.569 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 PILATUS 6M 2023-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
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 2.55 43.95 99.88 0.14 0.16 0.09 0.995 8.14 3.5 69425 33.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.551 2.642 99.75 0.66 0.78 0.858 2
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 2.55 43.95 1.34 36709 1837 99.89 0.1872 0.1848 0.1851 0.2319 0.2313 33.41
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 13.1008 f_angle_d 0.6466 f_chiral_restr 0.0426 f_plane_restr 0.0048 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9204 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 200
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing