3HZT

Crystal structure of Toxoplasma gondii CDPK3, TGME49_105860


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DXNPDB entry 3DXN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529318% PEG 3350, 0.2 M KF, 3 mM SU11652, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.051α = 90
b = 43.761β = 96.95
c = 84.821γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97937APS19-ID

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
123099.70.0480.03326.633.6354093540926.9
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)
122.0396.60.4570.3692.6863.31693

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 3DXN2303538035380177099.380.210.210.2070.252RANDOM42.411
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]
3.13-1.03-1.12-2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.486
r_dihedral_angle_4_deg19.539
r_dihedral_angle_3_deg15.938
r_dihedral_angle_1_deg5.112
r_scangle_it2.883
r_scbond_it1.796
r_mcangle_it1.208
r_angle_refined_deg1.141
r_mcbond_it0.646
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.486
r_dihedral_angle_4_deg19.539
r_dihedral_angle_3_deg15.938
r_dihedral_angle_1_deg5.112
r_scangle_it2.883
r_scbond_it1.796
r_mcangle_it1.208
r_angle_refined_deg1.141
r_mcbond_it0.646
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3263
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms78

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JBluIce-EPICSdata collection