8XEU | pdb_00008xeu

Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrichrome bound

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HXP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	100 mM BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2	38.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.49	α = 90
b = 62.916	β = 90
c = 67.064	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		2021-03-17	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	1.8	42.9	99.4	0.096	0.027	0.999	20.4	13		24183

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	1.8	1.84	98		0.983	0.283	0.82	3	13.6

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	3HXP	1.8	33.555	24141	1161	99.207	0.182	0.1795	0.1873	0.2265	0.2289	24.395

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]
-0.634			0.733		-0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.207
r_dihedral_angle_4_deg	15.434
r_dihedral_angle_3_deg	13.825
r_dihedral_angle_1_deg	6.921
r_lrange_it	4.28
r_lrange_other	4.279
r_scangle_it	2.19
r_scangle_other	2.189
r_angle_refined_deg	1.746
r_angle_other_deg	1.427
r_scbond_it	1.364
r_scbond_other	1.364
r_mcangle_it	1.344
r_mcangle_other	1.344
r_mcbond_it	0.874
r_mcbond_other	0.87
r_symmetry_xyhbond_nbd_refined	0.23
r_nbd_other	0.228
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.212
r_nbtor_refined	0.174
r_symmetry_nbd_other	0.172
r_xyhbond_nbd_refined	0.154
r_xyhbond_nbd_other	0.138
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
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	257
Heterogen Atoms	49

Software

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