8J4J

X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with ferric ion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7W3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	0.2 M magnesium formate dihydrate, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.522	α = 90
b = 91.522	β = 90
c = 150.454	γ = 120

Symmetry
Space Group	P 63 2 2

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 EIGER X 16M		2022-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.899995	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.15	43.82	99.5	0.999	11.02	10.26		38034

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.16			0.789	1.19

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.15	43.78	19724	1052	99.44	0.17301	0.16944	0.24188	RANDOM	68.127

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]
-0.15	-0.08		-0.15		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.039
r_long_range_B_refined	12.159
r_long_range_B_other	12.029
r_dihedral_angle_2_deg	10.054
r_scangle_other	9.771
r_dihedral_angle_1_deg	6.957
r_scbond_it	6.937
r_scbond_other	6.917
r_mcangle_it	6.443
r_mcangle_other	6.442
r_mcbond_other	5.107
r_mcbond_it	5.106
r_angle_refined_deg	1.528
r_angle_other_deg	0.478
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2364
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing