4BHL

Crystal structure of Litopenaeus vannamei arginine kinase in binary complex with arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AM1PDB ENTRY 4AM1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % (W/V) PEG 8000 USING THE MICROBATCH METHOD
Crystal Properties
Matthews coefficientSolvent content
2.0339.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.368α = 90
b = 70.338β = 90
c = 82.054γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2701M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING2012-07-05MSINGLE 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
11.919.11000.0622.37.126516314.29
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)
11.92.0196.10.215.46.9

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 REPLACEMENTPDB ENTRY 4AM11.946.4611.9726365133699.990.17480.17210.226816.3
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]
0.9712-0.0398-0.9314
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.471
f_angle_d1.043
f_chiral_restr0.066
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2723
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms16

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing