4UOF

Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BE4PDB ENTRY 1BE4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% (W/V) PEG 4,000
Crystal Properties
Matthews coefficientSolvent content
2.449.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.11α = 90
b = 134.38β = 90
c = 104.76γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270TOROIDAL FOCUSING MIRROR2013-11-01MSINGLE 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
12.119.891.20.1415.47.826320220.42
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)
12.12.295.10.622.75.4

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 1BE42.10219.8541.3326423133490.720.19260.18950.249321.7
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.775
f_angle_d1.394
f_chiral_restr0.067
f_bond_d0.02
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3579
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms81

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing