8XFA

Structure of the siderophore periplasmic binding protein FtsB mutant Y137A from Streptococcus pyogenes with ferrioxamine E bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XEU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	100 mM KSCN 30% PEG MME-550

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.817	α = 90
b = 61.723	β = 90
c = 69.59	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	PIXEL	DECTRIS PILATUS3 S 2M		2022-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.85	46.2	99.1	0.103	0.03	0.999	18.6	12.6		22069

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89			0.851	0.292	0.729	2.4

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8XEU	1.85	46.177	22022	817	98.944	0.173	0.1714	0.2203	22.272

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]
-1.253			0.152		1.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.556
r_dihedral_angle_3_deg	13.487
r_dihedral_angle_1_deg	6.045
r_dihedral_angle_2_deg	4.768
r_lrange_it	4.667
r_lrange_other	4.639
r_scangle_it	3.784
r_scangle_other	3.783
r_scbond_it	2.378
r_scbond_other	2.377
r_mcangle_it	1.973
r_mcangle_other	1.972
r_angle_refined_deg	1.393
r_mcbond_it	1.339
r_mcbond_other	1.337
r_angle_other_deg	0.493
r_nbd_refined	0.216
r_symmetry_nbd_other	0.186
r_nbd_other	0.179
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.135
r_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
r_metal_ion_refined	0.064
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2191
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	49

Software

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