4M84

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1455


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SX9PDB ENTRY 3SX9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529824% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1455, pH 7.5, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.12α = 90
b = 73.18β = 99.77
c = 66.01γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2013-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL14-11.127SSRLBL14-1

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
11.99848.67394.60.058103.72894837.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3SX91.99848.6728905144894.190.2010.1980.257RANDOM54.6328
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]
-0.870.560.580.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.516
r_dihedral_angle_3_deg16.781
r_dihedral_angle_4_deg16.212
r_dihedral_angle_1_deg5.67
r_mcangle_it2.983
r_mcbond_it1.987
r_mcbond_other1.987
r_angle_refined_deg1.434
r_angle_other_deg0.794
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.516
r_dihedral_angle_3_deg16.781
r_dihedral_angle_4_deg16.212
r_dihedral_angle_1_deg5.67
r_mcangle_it2.983
r_mcbond_it1.987
r_mcbond_other1.987
r_angle_refined_deg1.434
r_angle_other_deg0.794
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3698
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms23

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction