7LAQ

Crystal structure of Campylobacter jejuni Cj0843c lytic transglycosylase in complex with N,N'-diacetylchitobiose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CF9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 sodium citrate buffer pH 5.1-6.0, and 25-33% PEG 600. The protein was concentrated to 10 mg/ml in 10 mM HEPES pH 8.0 and 200 mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.989	α = 90
b = 176.989	β = 90
c = 176.989	γ = 90

Symmetry
Space Group	I 2 3

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	DECTRIS EIGER X 16M		2020-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X17B1	0.97935	NSLS	X17B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.58	29.52	99.5	0.17	0.997	13	13.9		28913

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.58	2.65			1.018	0.782

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	6CF9	2.58	29.5	27339	1574	99.52	0.1786	0.1757	0.2287	RANDOM	42.196

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.186
r_dihedral_angle_4_deg	18.879
r_dihedral_angle_3_deg	17.923
r_dihedral_angle_1_deg	6.159
r_angle_refined_deg	1.523
r_angle_other_deg	1.292
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.186
r_dihedral_angle_4_deg	18.879
r_dihedral_angle_3_deg	17.923
r_dihedral_angle_1_deg	6.159
r_angle_refined_deg	1.523
r_angle_other_deg	1.292
r_chiral_restr	0.076
r_bond_refined_d	0.008
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	4276
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	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.