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Crystal structure of shikimate-3-phosphate and glyphosate bound 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Morpheus B5: 12% (v/v) PEG 500 MME: 8% (w/v) PEG 20000, 0.1M (Sodium HEPES: MOPS), 0.03 M Sodium fluoride: 0.03 M Sodium bromide: 0.03 M Sodium iodide), KlpnC.18288.a.B1.PW39049 at 20 mg/mL, Tray: plate 12156 well B5 drop 2, Puck: PSL0514, Cryo: direct
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.243 α = 90 b = 115.22 β = 90 c = 183.266 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 2021-10-19 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 1.26 97.54 96.7 0.054 0.059 0.023 0.999 14.9 6.4 241838 13.15
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 1.26 1.34 99.1 0.592 0.644 0.249 0.856 6.4
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 1G6T 1.26 32.51 1.35 241654 12028 96.61 0.1379 0.137 0.1383 0.1553 0.1564 16.9623
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 13.14 f_angle_d 0.995 f_chiral_restr 0.08 f_plane_restr 0.01 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6432 Nucleic Acid Atoms Solvent Atoms 1197 Heterogen Atoms 94
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction