3TNY

Structure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	312	Protein 10-20 mg/ml, 0.1M HEPES 7.0, 30% Jeffamine ED-2001. Direct cryoprotection. , VAPOR DIFFUSION, HANGING DROP, temperature 312K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.796	α = 90
b = 47.328	β = 112.88
c = 64.981	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 QUANTUM 315		2010-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97	ALS	5.0.2

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	1.55	50	99.5	0.118	9.2	7.3		46458

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.61

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.55	50	44098	2344	98.32	0.1731	0.1723	0.1891	RANDOM	21.1498

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]
0.01		-0.13	0.51		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.512
r_dihedral_angle_4_deg	20.361
r_dihedral_angle_3_deg	11.84
r_dihedral_angle_1_deg	5.488
r_scangle_it	2.48
r_scbond_it	1.465
r_angle_refined_deg	1.109
r_mcangle_it	0.86
r_angle_other_deg	0.823
r_mcbond_it	0.437

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.512
r_dihedral_angle_4_deg	20.361
r_dihedral_angle_3_deg	11.84
r_dihedral_angle_1_deg	5.488
r_scangle_it	2.48
r_scbond_it	1.465
r_angle_refined_deg	1.109
r_mcangle_it	0.86
r_angle_other_deg	0.823
r_mcbond_it	0.437
r_mcbond_other	0.076
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2170
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.