1YOL

Crystal structure of Src kinase domain in complex with CGP77675


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FMK1FMK/3LCK hybrid
experimental modelPDB 3LCK1FMK/3LCK hybrid

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
2.8857.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.53α = 100.38
b = 62.95β = 89.16
c = 72.79γ = 89.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
12.320960.0539.929676
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)
2.32.593.50.2035.2

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 REPLACEMENTTHROUGHOUT1FMK/3LCK hybrid2.32029675156297.130.195850.193120.24746RANDOM41.462
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]
-0.440.430.25-0.42-0.430.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.629
r_dihedral_angle_3_deg16.437
r_dihedral_angle_4_deg15.032
r_dihedral_angle_1_deg6.046
r_scangle_it2.55
r_angle_refined_deg1.688
r_scbond_it1.649
r_mcangle_it1.318
r_mcbond_it0.857
r_angle_other_deg0.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.629
r_dihedral_angle_3_deg16.437
r_dihedral_angle_4_deg15.032
r_dihedral_angle_1_deg6.046
r_scangle_it2.55
r_angle_refined_deg1.688
r_scbond_it1.649
r_mcangle_it1.318
r_mcbond_it0.857
r_angle_other_deg0.806
r_symmetry_vdw_other0.3
r_symmetry_vdw_refined0.28
r_symmetry_hbond_refined0.223
r_nbd_refined0.199
r_xyhbond_nbd_refined0.187
r_nbd_other0.181
r_nbtor_refined0.179
r_mcbond_other0.141
r_nbtor_other0.085
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4091
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
AMoREphasing