2WO6

Human Dual-Specificity Tyrosine-Phosphorylation-Regulated Kinase 1A in complex with a consensus substrate peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VX3PDB ENTRY 2VX3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2M SODIUM FORMATE, 20% PEG3350, 10% ETHYLENE GLYCOL, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8857.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.43α = 90
b = 168.43β = 90
c = 62.42γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
12.555.131000.1710.87.535283
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)
12.52.641000.523.76.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VX32.5403366716061000.190.1880.229RANDOM19.55
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]
-0.28-0.14-0.280.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.333
r_dihedral_angle_4_deg19.04
r_dihedral_angle_3_deg13.894
r_dihedral_angle_1_deg5.915
r_scangle_it2.691
r_scbond_it1.686
r_angle_refined_deg1.528
r_angle_other_deg1
r_mcangle_it0.942
r_mcbond_it0.509
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.333
r_dihedral_angle_4_deg19.04
r_dihedral_angle_3_deg13.894
r_dihedral_angle_1_deg5.915
r_scangle_it2.691
r_scbond_it1.686
r_angle_refined_deg1.528
r_angle_other_deg1
r_mcangle_it0.942
r_mcbond_it0.509
r_mcbond_other0.151
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5635
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing