5BJU

X-ray structure of the PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	22% PEG-5000, 2% MPD, 10 mM UDP, 100 mM MES

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.135	α = 90
b = 107.882	β = 90
c = 110.208	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker Platinum 135		2016-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	50	97.3	0.092	0.092	13.2	3.7		54971

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)	Redundancy	Number Unique Reflections (All)
1	2	2.1	93.4		0.253	0.253	4.6	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	30	52185	2728	97.35	0.19519	0.19303	0.23673	RANDOM	17.679

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]
-0.73			-0.27		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.642
r_dihedral_angle_4_deg	21.519
r_dihedral_angle_3_deg	15.703
r_dihedral_angle_1_deg	6.983
r_long_range_B_refined	6.065
r_long_range_B_other	6.064
r_scangle_other	4.554
r_scbond_it	2.858
r_scbond_other	2.857
r_mcangle_it	2.627
r_mcangle_other	2.627
r_mcbond_it	1.771
r_mcbond_other	1.75
r_angle_refined_deg	1.701
r_angle_other_deg	0.807
r_chiral_restr	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	5283
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing