5BXI

1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii with Tyrosine of Tag Bound to Active Site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O0N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6295Protein:7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: PACT (B10), 0.2 M Magnesium chloride, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 236.814α = 90
b = 73.4β = 116.83
c = 122.671γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97890APS21-ID-D

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
11.73098.50.0590.059224.9202729202729-328
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)
11.71.7399.90.4823.24.9

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 REPLACEMENTTHROUGHOUT4O0N1.729.981924401020398.230.155510.153610.1917RANDOM33.435
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]
-0.660.041.74-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.188
r_dihedral_angle_4_deg16.653
r_dihedral_angle_3_deg10.952
r_long_range_B_refined6.765
r_long_range_B_other6.765
r_dihedral_angle_1_deg3.858
r_scangle_other3.38
r_scbond_it2.258
r_scbond_other2.256
r_mcangle_it2.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.188
r_dihedral_angle_4_deg16.653
r_dihedral_angle_3_deg10.952
r_long_range_B_refined6.765
r_long_range_B_other6.765
r_dihedral_angle_1_deg3.858
r_scangle_other3.38
r_scbond_it2.258
r_scbond_other2.256
r_mcangle_it2.218
r_mcangle_other2.218
r_mcbond_it1.499
r_mcbond_other1.499
r_angle_refined_deg1.398
r_angle_other_deg0.79
r_chiral_restr0.092
r_gen_planes_refined0.022
r_gen_planes_other0.017
r_bond_refined_d0.01
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14647
Nucleic Acid Atoms
Solvent Atoms1854
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
BLU-MAXdata collection
PHASERphasing