Experiment: 4AM9

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VGY	PDB ENTRY 2VGY

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1898	0.2381	0.2335	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