1YOJ

Crystal structure of Src kinase domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otheractive Src kinase domain in complex with CGP77675

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529720% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.9358.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.867α = 100.52
b = 62.542β = 88.88
c = 73.902γ = 89.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00075SLSX06SA

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
11.952093.90.1356.851365
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)
1.952.290.40.3343.7

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 REPLACEMENTTHROUGHOUTactive Src kinase domain in complex with CGP776751.952048107254294.330.21620.214030.25811RANDOM27.65
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]
-0.93-0.07-0.11-1.70.112.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.384
r_dihedral_angle_4_deg18.866
r_dihedral_angle_3_deg15.907
r_dihedral_angle_1_deg6.029
r_scangle_it3.878
r_scbond_it2.533
r_mcangle_it1.672
r_angle_refined_deg1.496
r_mcbond_it1.054
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.384
r_dihedral_angle_4_deg18.866
r_dihedral_angle_3_deg15.907
r_dihedral_angle_1_deg6.029
r_scangle_it3.878
r_scbond_it2.533
r_mcangle_it1.672
r_angle_refined_deg1.496
r_mcbond_it1.054
r_nbtor_refined0.305
r_nbd_refined0.209
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.184
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3622
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing