3BYV

Crystal structure of Toxoplasma gondii specific rhoptry antigen kinase domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320% PEG 3350, 0.2 M MgNO3, 0.1 M Tris-HCl pH 8.5, 1 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2VAPOR DIFFUSION, SITTING DROP8.529324% PEG 3350, 0.2 M MgNO3, 0.1 M Tris-HCl pH 8.5, 1 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.072α = 90
b = 69.821β = 90
c = 85.418γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-24MSINGLE WAVELENGTH
21x-ray100IMAGE PLATERIGAKU RAXIS IV2007-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1
2ROTATING ANODERIGAKU FR-E+ DW2.29

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
1,21.84099.90.0690.0628.57.3334843348424.2
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)
1.81.861000.4860.4274.217.43306

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.836.443173131731169299.870.203340.203340.201720.23273RANDOM13.045
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]
-0.040.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.95
r_dihedral_angle_4_deg19.926
r_dihedral_angle_3_deg17.357
r_dihedral_angle_1_deg8.639
r_scangle_it4.75
r_scbond_it3.289
r_angle_refined_deg2.367
r_mcangle_it2.056
r_mcbond_it1.495
r_symmetry_hbond_refined0.372
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.95
r_dihedral_angle_4_deg19.926
r_dihedral_angle_3_deg17.357
r_dihedral_angle_1_deg8.639
r_scangle_it4.75
r_scbond_it3.289
r_angle_refined_deg2.367
r_mcangle_it2.056
r_mcbond_it1.495
r_symmetry_hbond_refined0.372
r_nbtor_refined0.314
r_symmetry_vdw_refined0.265
r_nbd_refined0.226
r_xyhbond_nbd_refined0.205
r_chiral_restr0.189
r_bond_refined_d0.028
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2846
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing