9EI7 | pdb_00009ei7

PasI from Photorhabdus asymbiotica bound to vanadyl, succinate, and 5-amino-6-hydroxy-octanosyl acid 2-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PasI was co-crystallized with vanadyl, AHOAP, and succinate in a hanging drop vapor diffusion experiment. The protein solution [10 mg/mL of His-PasI, 1 equiv of vanadyl sulfate, 5 equiv of sodium succinate, 5 equiv of AHOAP, 17 mM Tris pH 7.6, and 2% (v/v) glycerol] was mixed with the reservoir solution [0.1 M Bis-Tris (pH 5.5), 0.15 M Li2SO4, and 27% (w/v) PEG 3350] in a 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.106	α = 90
b = 104.23	β = 90
c = 39.954	γ = 90

Symmetry
Space Group	P 21 21 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		2024-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97934	NSLS-II	17-ID-2

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	1.48	52.12	99.9	0.996	8.7	8.2		39148			15.38

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	1.48	1.53			0.601

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.48	52.05	1.33	73937	3497	99.77	0.18	0.1783	0.1783	0.2143	0.2142

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.89
f_angle_d	1.246
f_chiral_restr	0.114
f_bond_d	0.013
f_plane_restr	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1784
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	43

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHENIX	phasing