4XW6

X-ray structure of PKAc with ADP, free phosphate ion, CP20, magnesium ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DH3 

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
2.3453.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.304α = 90
b = 79.228β = 90
c = 97.82γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.94098.60.04230.153.832017
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)
1.91.9791.90.3892.53.1

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 REPLACEMENTFREE R-VALUE4DH31.92032017159589.90.1860.1860.2646RANDOM
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
63302.2
RMS Deviations
KeyRefinement Restraint Deviation
s_anti_bump_dis_restr0.147
s_non_zero_chiral_vol0.096
s_zero_chiral_vol0.095
s_similar_adp_cmpnt0.08
s_angle_d0.032
s_from_restr_planes0.0305
s_bond_d0.015
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2957
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms65

Software

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