Experiment: 3DLU

Structures of SRP54 and SRP19, the two proteins assembling the ribonucleic core of the Signal Recognition Particle from the archaeon Pyrococcus furiosus.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		experimental phasing

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	273	1.2-1.3M Na Malonate, 100mM Na Acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.074	α = 90
b = 79.699	β = 107.65
c = 60.548	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 210		2005-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	.92004	ALS	8.3.1

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	1.8	50	99.8	0.069	0.069	14.9	4.1		37519	1	1	21

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)
	1.8	1.85	98.3		0.427	0.427	2.7	3.6	3075

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	experimental phasing	1.8	42	1	1	36384	36384	1987	96.6	0.2247	0.1905	0.1866	0.2247	0.2245	5.5% of all reflections	21

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]
-2.0554		-3.9811	-3.5784		5.6338

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.84
f_angle_d	1.03
f_chiral_restr	0.068
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2995
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	46

Software

Software
Software Name	Purpose
PHENIX	refinement
ELVES	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing