5J3U

Co-crystal structure of the regulatory domain of Toxoplasma gondii PKA with cAMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OF13OF1, 2QCS, 3TNP
experimental modelPDB 2QCS3OF1, 2QCS, 3TNP
experimental modelPDB 3TNP3OF1, 2QCS, 3TNP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529325% peg3350, 0.1M NH4Oac, 0.1M Hepes pH 7.5, 2 mM cAMP
Crystal Properties
Matthews coefficientSolvent content
2.2946.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.857α = 90
b = 59.414β = 90
c = 120.843γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979337APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.842.361000.0950.1010.0340.99919.28.725458
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)
11.81.841000.8748.9

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 REPLACEMENTTHROUGHOUT3OF1, 2QCS, 3TNP1.84124189122099.960.17120.16960.2042RANDOM22.494
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]
0.05-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.025
r_dihedral_angle_3_deg12.399
r_dihedral_angle_4_deg11.814
r_dihedral_angle_1_deg5.719
r_mcangle_it2.225
r_angle_refined_deg1.785
r_mcbond_it1.581
r_mcbond_other1.577
r_angle_other_deg0.981
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.025
r_dihedral_angle_3_deg12.399
r_dihedral_angle_4_deg11.814
r_dihedral_angle_1_deg5.719
r_mcangle_it2.225
r_angle_refined_deg1.785
r_mcbond_it1.581
r_mcbond_other1.577
r_angle_other_deg0.981
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2020
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms56

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing