6CN1

2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BQ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6292Protein: 1.4 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3, Screen: PACT (B10), 0.2M Magnesium chloride, 0.1M MES buffer pH 6.0, 20% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.0540.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.615α = 90
b = 148.119β = 90
c = 164.627γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.753099.40.1360.1360.1480.058136.482344-351.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.898.20.7910.7910.8630.3420.7142.26.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5BQ22.7529.9577560412799.270.211670.209510.25179RANDOM51.033
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]
-2.78-0.172.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.152
r_dihedral_angle_3_deg7.993
r_dihedral_angle_4_deg7.209
r_long_range_B_refined2.571
r_long_range_B_other2.557
r_dihedral_angle_1_deg1.657
r_angle_refined_deg1.202
r_mcangle_it1.101
r_mcangle_other1.101
r_scangle_other1.037
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.152
r_dihedral_angle_3_deg7.993
r_dihedral_angle_4_deg7.209
r_long_range_B_refined2.571
r_long_range_B_other2.557
r_dihedral_angle_1_deg1.657
r_angle_refined_deg1.202
r_mcangle_it1.101
r_mcangle_other1.101
r_scangle_other1.037
r_angle_other_deg0.869
r_scbond_it0.615
r_scbond_other0.615
r_mcbond_it0.614
r_mcbond_other0.614
r_chiral_restr0.076
r_gen_planes_refined0.022
r_gen_planes_other0.02
r_bond_refined_d0.007
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25218
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms437

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing