3N51

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor RM-1-95


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I7B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529824% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0439.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.523α = 90
b = 72.754β = 98.88
c = 66.024γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.976SSRLBL7-1

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
12.15099.90.0946.63.826020541.3
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)
2.12.1899.90.7991.13.82590

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 SYNTHESISTHROUGHOUT3i7b2.139.4526002132599.880.1960.1930.242RANDOM50.291
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]
-0.10.870.41-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.67
r_dihedral_angle_4_deg19.377
r_dihedral_angle_3_deg14.053
r_dihedral_angle_1_deg5.182
r_scangle_it5.099
r_scbond_it3.509
r_mcangle_it2.747
r_mcbond_it1.754
r_angle_refined_deg1.124
r_angle_other_deg0.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.67
r_dihedral_angle_4_deg19.377
r_dihedral_angle_3_deg14.053
r_dihedral_angle_1_deg5.182
r_scangle_it5.099
r_scbond_it3.509
r_mcangle_it2.747
r_mcbond_it1.754
r_angle_refined_deg1.124
r_angle_other_deg0.801
r_mcbond_other0.544
r_chiral_restr0.062
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3613
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms36

Software

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