8XF4 | pdb_00008xf4

Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with Bisucaberin 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	150 mM KSCN 30% PEG-MME 2000

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.974	α = 90
b = 62.099	β = 90
c = 67.926	γ = 90

Symmetry
Space Group	P 21 21 21

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	2	45.8	98.6	0.075	0.021	1	25.2	13.2		17418

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	2	2.05			0.996	0.281	0.817	2.9

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	2	45.8	17386	829	98.259	0.201	0.1991	0.2057	0.234	0.2381	35.564

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]
-1.529			-0.303		1.832

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.393
r_dihedral_angle_3_deg	14.418
r_lrange_it	6.698
r_lrange_other	6.69
r_dihedral_angle_1_deg	6.33
r_scangle_it	5.31
r_scangle_other	5.309
r_dihedral_angle_2_deg	4.682
r_mcangle_it	3.415
r_mcangle_other	3.415
r_scbond_it	3.317
r_scbond_other	3.315
r_mcbond_it	2.388
r_mcbond_other	2.388
r_angle_refined_deg	1.529
r_angle_other_deg	0.515
r_symmetry_nbd_refined	0.266
r_nbd_refined	0.223
r_nbd_other	0.216
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.138
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.067
r_metal_ion_refined	0.057
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.006
r_gen_planes_refined	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	2183
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	58

Software

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