5U4H

1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Protein: 17.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: JCSG+ (F8), 2.1M DL-Malic acid (pH 7.0); Cryo: 4M Sodium formate.
Crystal Properties
Matthews coefficientSolvent content
2.0840.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.289α = 90
b = 70.085β = 110.05
c = 78.109γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-06-30MSINGLE 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)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
11.052099.50.0640.06416.94357259-37.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.0799.40.6250.9192.53.8

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 REPLACEMENTTHROUGHOUT5BQ21.0519.963387461792999.380.162260.161560.17561RANDOM11.965
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]
-0.18-0.13-0.090.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.895
r_sphericity_free17.23
r_dihedral_angle_4_deg11.16
r_dihedral_angle_3_deg11.025
r_sphericity_bonded4.943
r_dihedral_angle_1_deg4.47
r_long_range_B_refined1.862
r_long_range_B_other1.862
r_angle_refined_deg1.458
r_rigid_bond_restr1.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.895
r_sphericity_free17.23
r_dihedral_angle_4_deg11.16
r_dihedral_angle_3_deg11.025
r_sphericity_bonded4.943
r_dihedral_angle_1_deg4.47
r_long_range_B_refined1.862
r_long_range_B_other1.862
r_angle_refined_deg1.458
r_rigid_bond_restr1.159
r_angle_other_deg0.84
r_scangle_other0.835
r_scbond_it0.649
r_scbond_other0.649
r_mcangle_it0.568
r_mcangle_other0.568
r_mcbond_it0.398
r_mcbond_other0.398
r_chiral_restr0.088
r_gen_planes_refined0.021
r_gen_planes_other0.018
r_bond_refined_d0.008
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6286
Nucleic Acid Atoms
Solvent Atoms1197
Heterogen Atoms41

Software

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