2XUZ | pdb_00002xuz

Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferri-Enterobactin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WHY	PDB ENTRY 2WHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.2		PROTEIN WAS CRYSTALLIZED FROM 34% (V/V) PEG 600, 100 MM PHOSPHATE-CITRATE, PH 5.20

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.44	α = 90
b = 63.56	β = 100.65
c = 56.52	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC CCD	TOROIDAL MIRROR	2010-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.9	41.83	99.1	0.06	14.8	3.1		19907		-3	21.445

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	1.9	2	97.7		0.49	2.5	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2WHY	1.9	41.83	18136	1754	99.04	0.18974	0.18466	0.19	0.2432	0.25	RANDOM	22.421

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]
2.19		1.4	-2.46		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.378
r_dihedral_angle_3_deg	13.293
r_dihedral_angle_4_deg	10.05
r_dihedral_angle_1_deg	5.007
r_scangle_it	2.122
r_scbond_it	1.307
r_angle_refined_deg	1.213
r_angle_other_deg	0.814
r_mcangle_it	0.806
r_mcbond_it	0.448
r_mcbond_other	0.098
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2156
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	81

Software

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