3NYU

X-ray crystal structure of the Wbpe (WlbE) aminotransferase from pseudomonas aeruginosa as the PLP internal aldimine adduct with lysine 185


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NYSPDB ENTRY 3NYS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629825% pentaerythritol propoxylate, 100 mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1643.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.628α = 84.26
b = 54.068β = 82.43
c = 150.903γ = 64.93
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2009-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.99187APS19-BM

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
11.550930.0470.04744.22.3200622200622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.53870.090.0910.229398

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 3NYS1.501302006212006211011592.960.182870.182870.180910.21945RANDOM16.789
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]
0.410.3-0.9-0.17-0.1-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.965
r_dihedral_angle_4_deg23.159
r_dihedral_angle_3_deg13.775
r_dihedral_angle_1_deg6.536
r_scangle_it5.042
r_scbond_it3.431
r_mcangle_it2.188
r_angle_refined_deg1.634
r_mcbond_it1.521
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.965
r_dihedral_angle_4_deg23.159
r_dihedral_angle_3_deg13.775
r_dihedral_angle_1_deg6.536
r_scangle_it5.042
r_scbond_it3.431
r_mcangle_it2.188
r_angle_refined_deg1.634
r_mcbond_it1.521
r_chiral_restr0.112
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10950
Nucleic Acid Atoms
Solvent Atoms1489
Heterogen Atoms22

Software

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