7W8F

Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EFD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	30%(w/v) PEG-3,350, 50mM MgCl2, 0.1M Bis-Tris pH6.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.8	α = 90
b = 57.89	β = 95.02
c = 62.7	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	130	IMAGE PLATE	RIGAKU RAXIS VII		2021-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.85	26.3	97.6	0.085	10.6	3.48		20814

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92			0.345

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	1EFD	1.9	26.103	19251	982	97.775	0.179	0.1765	0.2187	25.187

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]
-0.017		-0.009	0.004		0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.234
r_dihedral_angle_4_deg	25.54
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_1_deg	6.212
r_lrange_it	6.099
r_lrange_other	6.085
r_scangle_it	4.868
r_scangle_other	4.866
r_scbond_it	3.039
r_scbond_other	3.037
r_mcangle_it	2.67
r_mcangle_other	2.67
r_mcbond_it	1.861
r_mcbond_other	1.845
r_angle_refined_deg	1.628
r_angle_other_deg	1.377
r_symmetry_xyhbond_nbd_refined	0.279
r_nbd_refined	0.204
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.184
r_nbd_other	0.178
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_other	0.146
r_chiral_restr	0.127
r_symmetry_nbtor_other	0.078
r_metal_ion_refined	0.043
r_bond_refined_d	0.009
r_gen_planes_refined	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	2174
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	41

Software

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