7TM5

Crystal structure of shikimate-3-phosphate 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 C5: 12% (v/v) PEG 500 MME: 8% (w/v) PEG 20000, 0.1M (Sodium HEPES: MOPS), 0.03 M Sodium nitrate, 0.03 M Sodium phosphate dibasic, 0.03 M Ammonium sulfate, KlpnC.18288.a.B1.PW39049 at 20 mg/mL, Tray: plate 12156 well C5 drop 1, Puck: PSL0602, Cryo: direct
Crystal Properties
Matthews coefficientSolvent content
2.4950.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.256α = 90
b = 115.387β = 90
c = 183.599γ = 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
11.4197.71000.0660.0720.0280.99914.36.518139914.56
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)
11.411.4999.90.6710.7340.2930.8116.2

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 REPLACEMENTTHROUGHOUT1G6T1.4135.861.35181234883699.930.13460.13330.160418.4412
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_d13.333
f_angle_d1.026
f_chiral_restr0.079
f_plane_restr0.008
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6444
Nucleic Acid Atoms
Solvent Atoms1242
Heterogen Atoms103

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction