1U54

Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U46 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5291PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.345.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 200.384α = 90
b = 42.332β = 96.28
c = 70.848γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
12.838.7198.30.05812.93.614697
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)
12.82.997.80.3193.73.64

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 REPLACEMENTTHROUGHOUT1U462.838.711469768498.30.2260.2220.322RANDOM27.15
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]
0.261.562.98-2.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.343
r_scangle_it2.29
r_angle_refined_deg1.972
r_scbond_it1.51
r_angle_other_deg0.912
r_mcangle_it0.896
r_mcbond_it0.515
r_symmetry_vdw_other0.26
r_nbd_refined0.252
r_nbd_other0.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.343
r_scangle_it2.29
r_angle_refined_deg1.972
r_scbond_it1.51
r_angle_other_deg0.912
r_mcangle_it0.896
r_mcbond_it0.515
r_symmetry_vdw_other0.26
r_nbd_refined0.252
r_nbd_other0.231
r_symmetry_vdw_refined0.23
r_xyhbond_nbd_refined0.188
r_symmetry_hbond_refined0.128
r_chiral_restr0.094
r_nbtor_other0.093
r_metal_ion_refined0.083
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4217
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing