Experiment: 2R3Y

Crystal structure of the DegS protease in complex with the YWF activating peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SOZ	PDB entry 1soz

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	The YWF (100 microM) was added to DegS and incubated 30 minutes before setting up the co-crystallization trials. Crystals of the complex were grown in sitting drops at 19 C by mixing 4 microL of DegS/YWF with 2 microL of a crystallization solution containing 0.1 M HEPES (pH 7.5), 6% PEG 6000, 9% MPD and 10 mM MgCl2. Crystal trials were set up in cryschem plates with a reservoir volume of 400 microL. , VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 205.8	α = 90
b = 142.7	β = 90.68
c = 41.1	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2006-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	30	95	0.044	0.047	13.2	2.8	39228	39228			60

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	88.2		0.32	0.33	2	2.6	3644

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1soz	2.5	15	38774	38774	1923	95	0.208	0.208	0.204	0.204	0.234	0.2324	random

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
c_angle_deg	1.45
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6292
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling