8XF7 | pdb_00008xf7

High-resolution structure of the siderophore periplasmic binding protein FtsB 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	0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.091	α = 90
b = 76.091	β = 90
c = 102.375	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		2022-05-27	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	1.12	40.42	99.9	0.047	0.011	0.75	18.6	18.6		128565

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	1.12	1.14	98.9		0.961	0.326	0.75	2.3	9.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8XEU	1.12	40.42	128487	2634	99.943	0.126	0.1252	0.1251	0.1403	0.1402	13.919

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]
0.09	0.045		0.09		-0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.362
r_dihedral_angle_3_deg	12.236
r_lrange_it	11.102
r_lrange_other	9.801
r_dihedral_angle_1_deg	6.405
r_scangle_it	6.294
r_scangle_other	6.293
r_dihedral_angle_2_deg	4.736
r_scbond_it	4.215
r_scbond_other	4.214
r_mcangle_other	4.016
r_mcangle_it	4.007
r_mcbond_it	2.693
r_mcbond_other	2.683
r_rigid_bond_restr	2.507
r_angle_refined_deg	1.637
r_angle_other_deg	0.561
r_symmetry_nbd_refined	0.254
r_nbd_refined	0.232
r_symmetry_xyhbond_nbd_refined	0.216
r_metal_ion_refined	0.208
r_nbtor_refined	0.183
r_symmetry_nbd_other	0.182
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.135
r_symmetry_metal_ion_refined	0.101
r_symmetry_xyhbond_nbd_other	0.096
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.078
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	421
Heterogen Atoms	59

Software

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