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)
TypeSourceAccession CodeDetails
in silico modelOtherA THEORETICAL MOLECULAR MODEL OF THE SHRIMP AMINO ACID SEQUENCE GENBANK ABI98020.1 BUILT WITH MOE CHEMCOMP AS A STARTING MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.40.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.1141.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.72α = 90
b = 70.39β = 90
c = 81.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDDOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6ANSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.25301000.0522.257.169131416.418
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.281000.543.967.1

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTA THEORETICAL MOLECULAR MODEL OF THE SHRIMP AMINO ACID SEQUENCE GENBANK ABI98020.1 BUILT WITH MOE CHEMCOMP AS A STARTING MODEL1.2528.0951.3391313457399.960.16070.15840.196816.07
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.531
f_angle_d1.339
f_chiral_restr0.074
f_bond_d0.012
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2733
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing