4BG4 | pdb_00004bg4

Crystal structure of Litopenaeus vannamei arginine kinase in a ternary analog complex with arginine, ADP-Mg and NO3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AM1	PDB ENTRY 4AM1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE AND 30 % (W/V) PEG 8000 PH 6.5 AT 289 K USING HANGING DROP METHOD.

Crystal Properties
Matthews coefficient	Solvent content
2	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.32	α = 90
b = 67.15	β = 92.12
c = 78.77	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	100	CCD	ADSC CCD	TOROIDAL FOCUSING MIRROR	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	1.6	14.8	99	0.06	20.9	6.3		86201		1.36	11.73

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	1.6	14.8	98		0.33	4.9	6.3

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 4AM1	1.601	14.847	1.36	86199	4322	99.3	0.1932	0.1914	0.18	0.2248	0.22

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]
-0.1488		0.0692	0.2607		-0.1119

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.661
f_angle_d	1.206
f_chiral_restr	0.074
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5642
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	96

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.