8XFI | pdb_00008xfi

High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine E bound (crystal form 2)

X-RAY DIFFRACTION

---

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, SITTING DROP		293.15	100 mM BIS-TRIS pH 5.5 200 mM Magnesium choride 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.415	α = 90
b = 70.571	β = 110.658
c = 69.073	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	PIXEL	DECTRIS PILATUS3 S 6M		2022-02-08	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	1.95	47.7	99.9	0.086	0.042	0.998	12.9	6.6		40353

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	1.95	2			0.883	0.379	0.73	2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8XEU	1.95	47.7	40336	2075	99.864	0.194	0.1915	0.1982	0.2322	0.2372	32.228

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]
-0.17		-0.273	0.606		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.93
r_dihedral_angle_3_deg	14.015
r_dihedral_angle_2_deg	7.472
r_dihedral_angle_1_deg	6.778
r_lrange_it	4.69
r_lrange_other	4.68
r_scangle_it	3.513
r_scangle_other	3.512
r_scbond_it	2.179
r_scbond_other	2.179
r_mcangle_it	2.092
r_mcangle_other	2.092
r_angle_refined_deg	1.574
r_mcbond_it	1.398
r_mcbond_other	1.396
r_angle_other_deg	0.533
r_nbd_other	0.223
r_nbd_refined	0.22
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.139
r_symmetry_nbd_refined	0.118
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_metal_ion_refined	0.068
r_xyhbond_nbd_other	0.039
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4372
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	88

Software

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