3GPE

Crystal Structure Analysis of PKC (alpha)-C2 domain complexed with Ca2+ and PtdIns(4,5)P2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DSYC2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 8000, 50mM potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7254.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.848α = 90
b = 57.848β = 90
c = 90.479γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray96CCDADSC QUANTUM 42007-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.930990.0613.341414022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9297.30.4641.6

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 REPLACEMENTTHROUGHOUTC2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE2201156660998.80.244340.242740.2773RANDOM16.343
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]
-0.08-0.04-0.080.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.332
r_dihedral_angle_3_deg9.422
r_dihedral_angle_4_deg8.357
r_dihedral_angle_1_deg4.423
r_angle_refined_deg0.707
r_scangle_it0.641
r_scbond_it0.384
r_mcangle_it0.259
r_mcbond_it0.131
r_chiral_restr0.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.332
r_dihedral_angle_3_deg9.422
r_dihedral_angle_4_deg8.357
r_dihedral_angle_1_deg4.423
r_angle_refined_deg0.707
r_scangle_it0.641
r_scbond_it0.384
r_mcangle_it0.259
r_mcbond_it0.131
r_chiral_restr0.038
r_bond_refined_d0.002
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1124
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms32

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling