3DFA

Crystal structure of kinase domain of calcium-dependent protein kinase cgd3_920 from Cryptosporidium parvum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QG5PDB entry 2QG5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62930.1 M Tris-HCl pH 7.6, 20% PEG 8000, 0.38 M Ammonium sulfate, 25% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4950.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.447α = 90
b = 69.447β = 90
c = 137.414γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.91996APS23-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
12.455096.90.0720.06411.213.2126411264159.4
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)
12.452.5483.50.4710.4114.5311.11058

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 REPLACEMENTTHROUGHOUTPDB entry 2QG52.4549.09125901259061196.940.2340.2340.2330.263RANDOM36.985
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]
-3.14-3.146.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.021
r_dihedral_angle_3_deg16.001
r_dihedral_angle_4_deg15.833
r_dihedral_angle_1_deg4.848
r_angle_refined_deg1.014
r_scangle_it0.926
r_scbond_it0.586
r_mcangle_it0.382
r_nbtor_refined0.299
r_symmetry_hbond_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.021
r_dihedral_angle_3_deg16.001
r_dihedral_angle_4_deg15.833
r_dihedral_angle_1_deg4.848
r_angle_refined_deg1.014
r_scangle_it0.926
r_scbond_it0.586
r_mcangle_it0.382
r_nbtor_refined0.299
r_symmetry_hbond_refined0.222
r_mcbond_it0.205
r_nbd_refined0.18
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_refined0.12
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2104
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection