5TW9 | pdb_00005tw9

1.50 Angstrom Crystal Structure of C-terminal Fragment (residues 322-384) of Iron Uptake System Component EfeO from Yersinia pestis.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 14.1 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (E3), 0.2M Sodium iodide, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.037	α = 90
b = 64.001	β = 90
c = 173.151	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	CCD	MARMOSAIC 300 mm CCD	C(111)	2016-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	30	100	0.067	0.067	43.4	7.2		62217		-3	18.8

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	1.5	1.53	100		0.66	0.933	3.8	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.5	29.61	58666	3112	99.94	0.17442	0.17293	0.18	0.2025	0.21	RANDOM	22.542

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]
0.28			0.73		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.312
r_sphericity_bonded	19.256
r_sphericity_free	19.019
r_dihedral_angle_4_deg	15.435
r_rigid_bond_restr	12.991
r_dihedral_angle_3_deg	10.654
r_long_range_B_refined	4.772
r_long_range_B_other	4.573
r_dihedral_angle_1_deg	2.834
r_scangle_other	1.872
r_mcangle_other	1.601
r_mcangle_it	1.6
r_angle_refined_deg	1.278
r_scbond_it	1.171
r_scbond_other	1.171
r_mcbond_it	0.927
r_mcbond_other	0.921
r_angle_other_deg	0.813
r_chiral_restr	0.075
r_gen_planes_refined	0.025
r_gen_planes_other	0.021
r_bond_refined_d	0.009
r_bond_other_d	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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2928
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing