7N7A

crystal structure of the dTDP-Qui3N N-formyltransferase from Helicobacter canadensis, apo form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LXQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	11-14% PEG-8000, 2% DMSO, 100 mM homopipes (pH 5)

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.956	α = 90
b = 74.701	β = 113.74
c = 82.284	γ = 90

Symmetry
Space Group	C 1 2 1

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		2019-10-04	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	1.8	50	99.3	0.059	18.7	7.6		65901

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	1.8	1.87	99.7		0.267	3.9	4.4

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	4lxq	1.8	29.67	62669	3232	99.3	0.169	0.1673	0.2037	RANDOM	20.084

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	35.831
r_dihedral_angle_4_deg	15.401
r_dihedral_angle_3_deg	13.681
r_dihedral_angle_1_deg	7.916
r_angle_refined_deg	1.618
r_angle_other_deg	1.406
r_chiral_restr	0.083
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	35.831
r_dihedral_angle_4_deg	15.401
r_dihedral_angle_3_deg	13.681
r_dihedral_angle_1_deg	7.916
r_angle_refined_deg	1.618
r_angle_other_deg	1.406
r_chiral_restr	0.083
r_bond_refined_d	0.011
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	4475
Nucleic Acid Atoms
Solvent Atoms	695
Heterogen Atoms	28

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 R01GM157729.