7TM6

Crystal structure of shikimate-3-phosphate and glyphosate bound 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G6T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291Morpheus 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 coefficientSolvent content
2.4850.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.243α = 90
b = 115.22β = 90
c = 183.266γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 19-ID0.97949NSLS-II19-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2697.5496.70.0540.0590.0230.99914.96.424183813.15
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)RedundancyNumber Unique Reflections (All)
11.261.3499.10.5920.6440.2490.8566.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1G6T1.2632.511.352416541202896.610.13790.1370.155316.9623
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.14
f_angle_d0.995
f_chiral_restr0.08
f_plane_restr0.01
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6432
Nucleic Acid Atoms
Solvent Atoms1197
Heterogen Atoms94

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction