3NVS

1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G6SPDB ENTRY 1G6S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein: 4.0 mGr/mL, 0.25M Sodium cloride, 0.01M Tris-HCl (pH 8.3), 2mM Glyphosate, 1mM Shikimate-3-phosphate; Screen: Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.5), 25% (w/v) PEG3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.8935.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.866α = 90
b = 87.484β = 105.26
c = 49.994γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2010-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.82648APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.021597.20.04416.32.2178530178530-36.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.021.0495.50.3912.22.28695

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1G6S1.02114.89169410169410897597.170.115250.115250.114060.13767RANDOM8.505
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]
-0.39-0.210.20.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.345
r_dihedral_angle_4_deg16.118
r_dihedral_angle_3_deg10.672
r_dihedral_angle_1_deg5.421
r_scangle_it5.008
r_scbond_it3.523
r_mcangle_it2.363
r_mcbond_other2.137
r_rigid_bond_restr1.808
r_mcbond_it1.687
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.345
r_dihedral_angle_4_deg16.118
r_dihedral_angle_3_deg10.672
r_dihedral_angle_1_deg5.421
r_scangle_it5.008
r_scbond_it3.523
r_mcangle_it2.363
r_mcbond_other2.137
r_rigid_bond_restr1.808
r_mcbond_it1.687
r_angle_refined_deg1.542
r_angle_other_deg0.979
r_chiral_restr0.099
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3240
Nucleic Acid Atoms
Solvent Atoms747
Heterogen Atoms65

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling