4F36

Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R9LPDB ENTRY 3R9l

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7290EBS internal tracking number 233837B2: JCSG B2, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, crystallant: 20% PEG3350, 200 mM sodium isothiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.46α = 90
b = 123.67β = 90
c = 145.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.0331710SSRLBL7-1

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
12.35098.80.07712.474.342511-344.419
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)
12.32.3691.30.4862.33.11

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 3R9l2.35042483214498.920.20.1980.235RANDOM40.762
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]
-0.63-1.892.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.429
r_dihedral_angle_4_deg24.369
r_dihedral_angle_3_deg13.369
r_dihedral_angle_1_deg6.082
r_angle_refined_deg1.411
r_angle_other_deg1.232
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.429
r_dihedral_angle_4_deg24.369
r_dihedral_angle_3_deg13.369
r_dihedral_angle_1_deg6.082
r_angle_refined_deg1.411
r_angle_other_deg1.232
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6311
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms3

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction