Experiment: 4AM1

Crystal structure of the marine crustacean decapod shrimp (Litopenaeus vannamei) arginine kinase in the absence of substrate or ligands.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		A THEORETICAL MOLECULAR MODEL OF THE SHRIMP AMINO ACID SEQUENCE GENBANK ABI98020.1 BUILT WITH MOE CHEMCOMP AS A STARTING MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.72	α = 90
b = 70.39	β = 90
c = 81.99	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC CCD	DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.	2012-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A		NSLS	X6A

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	1.25	30	100	0.05	22.25	7.16		91314			16.418

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	1.25	1.28	100		0.54	3.96	7.1

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	A THEORETICAL MOLECULAR MODEL OF THE SHRIMP AMINO ACID SEQUENCE GENBANK ABI98020.1 BUILT WITH MOE CHEMCOMP AS A STARTING MODEL	1.25	28.095	1.33	91313	4573	99.96	0.1607	0.1584	0.1747	0.1968	0.2121	16.07

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]
0.1012			-0.0593		-0.0419

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.531
f_angle_d	1.339
f_chiral_restr	0.074
f_bond_d	0.012
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2733
Nucleic Acid Atoms
Solvent Atoms	547
Heterogen Atoms

Software

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