4XW4

X-ray structure of PKAc with AMPPNP, SP20, calcium ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277100 mM MES pH 6.5, 5 mM DTT, 15-20% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.2952.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.364α = 90
b = 78.816β = 90
c = 97.985γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
11.824097.80.03633.083.836595
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)
1.821.8994.40.4672.23.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.82203659536595183291.90.18350.1840.2397RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
23297
RMS Deviations
KeyRefinement Restraint Deviation
s_anti_bump_dis_restr0.095
s_similar_adp_cmpnt0.08
s_non_zero_chiral_vol0.066
s_zero_chiral_vol0.051
s_angle_d0.027
s_from_restr_planes0.0235
s_bond_d0.011
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2917
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms64

Software

Software
Software NamePurpose
PHASERphasing
SHELXrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
SHELXL-97refinement