8ARB | pdb_00008arb

Heterologous Complex of shortened Aeromonas hydrophila Type III secretion substrate AscX with Yersinia enterocolitica chaperone YscY

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	reservoir solution: 0.1 M Hepes pH 7.5, 0.6-0.9 M sodium dihydrogen phosphate, 0.6-0.9 M potassium dihydrogen phosphate [1.4-1.8 M total phosphate]; protein: 10 mg/mL in 20 mM Tris pH 8, 150 mM NaCl, 5 mM TCEP; drop size: 0.66 uL protein + 0.33 uL reservoir

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.33	α = 90
b = 160.56	β = 90
c = 156.74	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS 6M-F		2020-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9919	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.63	80.28	99.3	0.229	0.996	9.3	24.86		34253			80.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.63	2.7	92.6		4.831	0.239	0.61	12.93

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7QIH	2.63	80.28	1.33	33394	1664	97.98	0.293	0.2912	0.29	0.3262	0.33	108.73

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	9.5589
f_angle_d	0.3579
f_chiral_restr	0.0279
f_plane_restr	0.0028
f_bond_d	0.0017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5266
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	35

Software

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