3E3K

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZLQ	PDB ENTRY 1ZLQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	293	1.5M ammonium sulfate, 0.1M sodium acetate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.7	α = 90
b = 158.7	β = 90
c = 134.6	γ = 120

Symmetry
Space Group	P 62

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	ADSC QUANTUM 4	mirrors	2007-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.9310	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8		93.6	0.053	24.9	4.9				2	64.602

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	89.7		0.348	5.3	5	4202

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 1ZLQ	2.8	48.45	44771	2356	100	0.24853	0.24475	0.32087	RANDOM	61.426

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]
0.33	0.16		0.33		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.198
r_dihedral_angle_3_deg	22.252
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_1_deg	8.972
r_scangle_it	3.123
r_angle_refined_deg	2.182
r_mcangle_it	2.164
r_scbond_it	2.065
r_mcbond_it	1.292
r_nbtor_refined	0.352

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.198
r_dihedral_angle_3_deg	22.252
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_1_deg	8.972
r_scangle_it	3.123
r_angle_refined_deg	2.182
r_mcangle_it	2.164
r_scbond_it	2.065
r_mcbond_it	1.292
r_nbtor_refined	0.352
r_nbd_refined	0.32
r_symmetry_vdw_refined	0.257
r_xyhbond_nbd_refined	0.256
r_symmetry_hbond_refined	0.196
r_chiral_restr	0.14
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11879
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	90

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.