8XF9

High-resolution structure of the siderophore periplasmic binding protein FtsB mutant Y137A 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% PEG MME-550

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.847	α = 90
b = 75.847	β = 90
c = 102.622	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	1.15	40.4	100	0.062	0.014	1	24.6	19.4		118354

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			1.19	0.341	0.732	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.15	40.4	118277	2410	99.996	0.1314	0.1311	0.1468	14.173

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]
0.06	0.03		0.06		-0.194

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.013
r_dihedral_angle_3_deg	12.444
r_lrange_it	10.667
r_lrange_other	9.615
r_scangle_it	6.848
r_scangle_other	6.782
r_dihedral_angle_1_deg	5.772
r_scbond_it	4.626
r_scbond_other	4.57
r_dihedral_angle_2_deg	4.36
r_mcangle_other	4.061
r_mcangle_it	4.057
r_rigid_bond_restr	2.926
r_mcbond_it	2.769
r_mcbond_other	2.762
r_angle_refined_deg	1.623
r_angle_other_deg	0.566
r_symmetry_nbd_refined	0.355
r_nbd_other	0.274
r_nbd_refined	0.232
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.18
r_metal_ion_refined	0.149
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.114
r_chiral_restr	0.087
r_symmetry_metal_ion_refined	0.086
r_symmetry_nbtor_other	0.078
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2215
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	45

Software

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