3I7B

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NM-PP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I79 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop vapor diffusion6.529826% PEG 3350, 0.18 M ammonium citrate, 4 mM NM-PP1; cryoprotected with 10% ethylene glycol, pH 6.5, sitting drop vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0239.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.243α = 90
b = 72.851β = 98.78
c = 65.713γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9885099.80.0658.34.230350529.7
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)
11.9882.0698.10.7411.94.12975

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 REPLACEMENTTHROUGHOUT3I791.9885030333153699.770.1940.1920.228RANDOM19.845
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]
0.340.780.67-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.84
r_dihedral_angle_4_deg18.445
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg4.557
r_scangle_it3.245
r_scbond_it2.054
r_mcangle_it1.724
r_mcbond_it0.985
r_angle_refined_deg0.878
r_angle_other_deg0.749
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.84
r_dihedral_angle_4_deg18.445
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg4.557
r_scangle_it3.245
r_scbond_it2.054
r_mcangle_it1.724
r_mcbond_it0.985
r_angle_refined_deg0.878
r_angle_other_deg0.749
r_mcbond_other0.245
r_chiral_restr0.05
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3694
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms40

Software

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