2DXE

Crystal structure of nucleoside diphosphate kinase in complex with GDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293Na Citrate, Bicine, 1mM GDP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.802α = 90
b = 69.802β = 90
c = 107.093γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.740.199.70.044397.332493-317.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7699.30.09

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2CWK1.740.0832449160999.80.1680.1680.19RANDOM17.3
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]
-0.460.37-0.460.92
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.5
c_scangle_it2.83
c_scbond_it1.91
c_mcangle_it1.57
c_angle_deg1.4
c_mcbond_it1.04
c_improper_angle_d0.81
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.5
c_scangle_it2.83
c_scbond_it1.91
c_mcangle_it1.57
c_angle_deg1.4
c_mcbond_it1.04
c_improper_angle_d0.81
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2491
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms33

Software

Software
Software NamePurpose
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing