8XET

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

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 100 mM MES pH 6.5 25% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.924	α = 90
b = 75.924	β = 90
c = 102.859	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		2022-03-23	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	1.11	40.5	100	0.055	0.013	1	25	18.1		132170

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	1.11	1.13	99.3		0.725	0.29	0.751	2.2	8.1

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	1.11	40.5	132091	2607	99.958	0.131	0.131	0.1424	14.208

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]
0.106	0.053		0.106		-0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.338
r_dihedral_angle_3_deg	14.065
r_lrange_it	11.333
r_lrange_other	9.699
r_scangle_it	6.999
r_scangle_other	6.997
r_dihedral_angle_1_deg	5.932
r_scbond_it	4.849
r_scbond_other	4.848
r_dihedral_angle_2_deg	4.8
r_mcangle_other	4.033
r_mcangle_it	4.028
r_rigid_bond_restr	2.981
r_mcbond_it	2.833
r_mcbond_other	2.823
r_angle_refined_deg	1.553
r_angle_other_deg	0.526
r_symmetry_nbd_refined	0.271
r_nbd_refined	0.232
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.182
r_metal_ion_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_metal_ion_refined	0.163
r_xyhbond_nbd_refined	0.161
r_nbd_other	0.152
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.079
r_gen_planes_refined	0.009
r_bond_refined_d	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	418
Heterogen Atoms	58

Software

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