4FKX

Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to CDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F36PDB ENTRY 4F36

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289TrbrA.00438.a.B1 PS01459 at 20.2 mg/mL against 40% MPD, 5% PEG8000, 0.1 M sodium cacodylate, pH 6.5, 2 mM CDP, 10 mM magnesium chloride, crystal tracking ID 234284b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2846.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.63α = 90
b = 121.37β = 90
c = 112.87γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+VariMax2012-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.75098.10.07932.778.55441253372-321.523
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)
11.71.7490.20.4383.24

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 4F361.741.3353338262898.090.15360.15210.1821RANDOM14.9271
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]
-0.120.060.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.928
r_dihedral_angle_4_deg24.263
r_dihedral_angle_3_deg11.387
r_dihedral_angle_1_deg5.715
r_angle_refined_deg1.525
r_angle_other_deg0.936
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.928
r_dihedral_angle_4_deg24.263
r_dihedral_angle_3_deg11.387
r_dihedral_angle_1_deg5.715
r_angle_refined_deg1.525
r_angle_other_deg0.936
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3526
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms86

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection