3SX9

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with Bumped Kinase Inhibitor, RM-1-132


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NYVPDB entry 3NYV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729826% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-132; frozen in LN2 after soaking in mother liquor supplemented with 10% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.281α = 90
b = 72.475β = 103.81
c = 67.267γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
12.65501000.1450.1459.8023.813349-350.5
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)
12.652.741000.8570.8571.5063.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3NYV2.6546.891333167799.460.19960.19710.244RANDOM44.9889
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]
0.291.65-2.112.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.32
r_angle_refined_deg0.907
r_angle_other_deg0.883
r_chiral_restr0.05
r_bond_refined_d0.007
r_bond_other_d0.005
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3664
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms30

Software

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