8XF8

High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine B

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	50 mM zinc sulfate 25% PEG 550-MME 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.223	α = 90
b = 76.223	β = 90
c = 102.502	γ = 120

Symmetry
Space Group	P 65

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		2022-10-16	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	1.15	40.5	94.9	0.058	0.019	0.999	20.9	10.3		113334

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	1.15	1.17	76.5		0.928	0.319	0.721	2.3

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	1.15	40.5	113330	2277	94.947	0.136	0.1353	0.1529	13.327

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]
0.099	0.05		0.099		-0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.078
r_dihedral_angle_3_deg	12.086
r_lrange_it	9.073
r_lrange_other	8.17
r_dihedral_angle_1_deg	6.143
r_scangle_it	5.286
r_scangle_other	5.285
r_mcangle_other	3.616
r_mcangle_it	3.61
r_scbond_it	3.408
r_scbond_other	3.402
r_dihedral_angle_2_deg	3.179
r_mcbond_it	2.368
r_mcbond_other	2.351
r_rigid_bond_restr	2.113
r_angle_refined_deg	1.669
r_dihedral_angle_other_2_deg	1.466
r_angle_other_deg	0.527
r_symmetry_nbd_refined	0.263
r_nbd_refined	0.233
r_metal_ion_refined	0.229
r_nbd_other	0.223
r_symmetry_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.183
r_symmetry_metal_ion_refined	0.132
r_xyhbond_nbd_refined	0.113
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.061
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2222
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	55

Software

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