4AM9

CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION CHAPERONE SYCD IN COMPLEX WITH A PEPTIDE OF THE TRANSLOCATOR YOPD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	RESERVOIR SOLUTION: 50 MM MES PH 6, 50 MM CITRATE PH 5, 1.1-1.4 M (NH4)2SO4. VAPOR DIFFUSION AT 293 K WITH DROP RATIO OF 1 TO 0.5 PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 8 MG/ML. 1.3 FOLD MOLAR EXCESS OF PEPTIDE OVER PROTEIN.

Crystal Properties
Matthews coefficient	Solvent content
4.82	74.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.369	α = 90
b = 106.369	β = 90
c = 51.998	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	MIRRORS	2011-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	2.5	25	99.4	0.11	18.5	14		11931			69.59

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	2.5	2.64	97		0.57	3.1	10

Refinement

Statistics
Diffraction ID	Structure Solution 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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2VGY	2.5	23.676	1.34	11901	588	99.32	0.1921	0.1899	0.2381	79.2

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]
5.2738			5.2738		-10.5477

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.576
f_angle_d	1.061
f_chiral_restr	0.069
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1116
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	35

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.