3NU8 | pdb_00003nu8

WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in Complex with the Internal Aldimine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NU7	PDB entry 3NU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	Crystallization conditions: 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350 in the reservoir; Protein solution contains 25 mM HEPES, pH 8.0, 100 mM NaCl, 0.5% glycerol; Incubated protein with 50 uM PLP prior to setting up tray; Drop made by mixing 1.5 uL of protein and reservoir solutions., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.786	α = 90
b = 148.723	β = 90
c = 53.215	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 270	Toroidal Focusing Mirror	2010-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.978	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.5	20	99.7	0.091	35.8	7.9		94182

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.53	99.8		0.662	3	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3NU7	1.5	19.83	94182	4948	99.71	0.19863	0.19733	0.1926	0.22281	0.2167	RANDOM	19.933

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]
			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.123
r_dihedral_angle_4_deg	15.59
r_dihedral_angle_3_deg	12.764
r_dihedral_angle_1_deg	5.202
r_scangle_it	2.16
r_scbond_it	1.242
r_angle_refined_deg	1.152
r_mcangle_it	0.799
r_mcbond_it	0.424
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5487
Nucleic Acid Atoms
Solvent Atoms	800
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling