3R9L

Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPKPDB ENTRY 1NPK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.9289GilaA.00438.a.A1 PW27083 at 24.97 mg/mL in 25 mM Hepes pH 7.0, 0.5 M NaCl, 5% glycerol, 2 mM DTT, 0.025% azide against CSHT C11 focus screen 0.1 M Hepes pH 7.0, 0.9 M Na phosphate, 0.9 M K phosphate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 216300h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.6265.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.96α = 90
b = 116.96β = 90
c = 62.69γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97946ALS5.0.1

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
12.655098.80.04926.025.677607665-360.858
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)
2.652.721000.5263.266567

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 1NPK2.6539.4761934898.260.23590.23440.2663RANDOM78.7938
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]
1.330.671.33-2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.361
r_dihedral_angle_4_deg28.396
r_dihedral_angle_3_deg14.313
r_dihedral_angle_1_deg6.811
r_scangle_it2.695
r_mcangle_it1.571
r_scbond_it1.539
r_angle_refined_deg1.278
r_mcbond_it0.854
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.361
r_dihedral_angle_4_deg28.396
r_dihedral_angle_3_deg14.313
r_dihedral_angle_1_deg6.811
r_scangle_it2.695
r_mcangle_it1.571
r_scbond_it1.539
r_angle_refined_deg1.278
r_mcbond_it0.854
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms813
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
XDSdata reduction