4O0N

2.4 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NDLPDB ENTRY 1NDL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5295Protein: 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (F6), 0.2M Ammonium sulfate, 0.1M PIS-TRIS pH 5.5, 25% (w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0239.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.385α = 90
b = 121.591β = 90
c = 212.274γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2013-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.43099.60.0840.08418.25.77509275092-351
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4499.80.5230.5233.25.83725

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NDL2.429.497101971019377199.530.194620.194620.192290.23791RANDOM48.676
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]
1.20.34-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.305
r_dihedral_angle_4_deg11.821
r_dihedral_angle_3_deg9.267
r_long_range_B_refined5.394
r_long_range_B_other5.26
r_scangle_other2.578
r_dihedral_angle_1_deg2.505
r_mcangle_it2.174
r_mcangle_other2.174
r_scbond_it1.685
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.305
r_dihedral_angle_4_deg11.821
r_dihedral_angle_3_deg9.267
r_long_range_B_refined5.394
r_long_range_B_other5.26
r_scangle_other2.578
r_dihedral_angle_1_deg2.505
r_mcangle_it2.174
r_mcangle_other2.174
r_scbond_it1.685
r_scbond_other1.587
r_mcbond_it1.363
r_mcbond_other1.362
r_angle_refined_deg1.219
r_angle_other_deg0.706
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14699
Nucleic Acid Atoms
Solvent Atoms548
Heterogen Atoms70

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling