3IS5

Crystal structure of CDPK kinase domain from toxoplasma Gondii, TGME49_018720


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.52930.1 M Glycine pH 9.5, 13.6% PEG8000, 0.2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9458.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.973α = 90
b = 113.973β = 90
c = 153.471γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.96427APS23-ID-B

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
12.4501000.0940.07185.8872308722254
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)
12.42.491000.9990.9171.855.88761

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 REPLACEMENTTHROUGHOUT3dxn2.55507270072046362299.10.220.220.2180.259RANDOM26.728
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]
0.130.060.13-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.541
r_dihedral_angle_3_deg17.704
r_dihedral_angle_4_deg17.427
r_dihedral_angle_1_deg5.391
r_scangle_it1.357
r_angle_refined_deg1.12
r_scbond_it0.743
r_mcangle_it0.483
r_mcbond_it0.254
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.541
r_dihedral_angle_3_deg17.704
r_dihedral_angle_4_deg17.427
r_dihedral_angle_1_deg5.391
r_scangle_it1.357
r_angle_refined_deg1.12
r_scbond_it0.743
r_mcangle_it0.483
r_mcbond_it0.254
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11865
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms237

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing