6VO8

X-ray structure of the Cj1427 in the presence of NADH and GDP-D-glycero-D-mannoheptose, an essential NAD-dependent dehydrogenase from Campylobacter jejuni

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	8-10% PEG-8000, 2%-tertbutyl alcohol, 100 mM homopipes, in the presence of 2.5 mM GDP-D-glycero-D-mannoheptose

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.723	α = 90
b = 98.852	β = 90
c = 72.939	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	100	PIXEL	Bruker PHOTON II		2019-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50	98.8	0.096	13.3	10.7		28260

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.5	97.5		0.351	3	4.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6vo6	2.4	30.01	26677	1590	98.86	0.2107	0.2063	0.2856	RANDOM	25.831

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]
0.03			-0.04		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.28
r_dihedral_angle_3_deg	17.82
r_dihedral_angle_4_deg	17.061
r_dihedral_angle_1_deg	8.493
r_angle_refined_deg	1.801
r_angle_other_deg	1.232
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.28
r_dihedral_angle_3_deg	17.82
r_dihedral_angle_4_deg	17.061
r_dihedral_angle_1_deg	8.493
r_angle_refined_deg	1.801
r_angle_other_deg	1.232
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4801
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	170

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.