3IDB

Crystal structure of (108-268)RIIb:C holoenzyme of cAMP-dependent protein kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ATPPDB entry 1ATP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION UNDER OIL (VDUO)7.52988% PEG 3350, 40 mM Bis-Tris pH 7.5, 0.05 mM Na Acetate, VAPOR DIFFUSION UNDER OIL (VDUO), temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2445.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.321α = 90
b = 65.733β = 99.95
c = 47.155γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.5200ALS8.2.2

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
11.625099.40.06830.388992216.9
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)
1.621.6899.10.486.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1ATP1.62508899299.40.2060.2060.2060.23RANDOM24.6
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]
0.460.323.16-3.62
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.3
c_angle_deg1.2
c_improper_angle_d0.71
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3926
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms33

Software

Software
Software NamePurpose
CNSrefinement
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
ADSCdata collection