8DAK

Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase from Campylobacter jejuni, serotype HS:3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	10-12% PEG8000, 0.75 M tetramethylammonium chloride, 100 mM homopiperazine-1,4-bis(2-ethanesulfonic acid), pH 5.0, protein pre-incubated with 5 mM GDP

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.534	α = 90
b = 67.932	β = 90
c = 96.125	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	PIXEL	Bruker PHOTON II		2021-07-20	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	1.5	50	97.5	0.094	11.4	5.7		63904

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	1.5	1.6	89.6		0.369	2.8	2.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 7M14	1.5	33.1	60748	3156	97.47	0.1932	0.1919	0.2188	RANDOM	9.26

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.565
r_dihedral_angle_4_deg	15.207
r_dihedral_angle_3_deg	13.926
r_dihedral_angle_1_deg	8.363
r_angle_refined_deg	1.596
r_angle_other_deg	1.374
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.565
r_dihedral_angle_4_deg	15.207
r_dihedral_angle_3_deg	13.926
r_dihedral_angle_1_deg	8.363
r_angle_refined_deg	1.596
r_angle_other_deg	1.374
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2882
Nucleic Acid Atoms
Solvent Atoms	496
Heterogen Atoms	93

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 U.S. National Science Foundation (DBI-2321666), 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.