1YOM

Crystal structure of Src kinase domain in complex with Purvalanol A


X-RAY DIFFRACTION

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
2.9558.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.698α = 100.61
b = 63.078β = 88.86
c = 74.055γ = 89.89
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 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
12.721.8930.1234.618966
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)
2.72.85950.4691.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.9121431274292.880.221870.217040.31322RANDOM44.857
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]
-3.321.3-0.11-1.81-0.15.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.741
r_scangle_it2.196
r_angle_refined_deg1.692
r_scbond_it1.253
r_mcangle_it1.188
r_angle_other_deg0.912
r_mcbond_it0.638
r_symmetry_vdw_other0.245
r_nbd_other0.222
r_nbd_refined0.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.741
r_scangle_it2.196
r_angle_refined_deg1.692
r_scbond_it1.253
r_mcangle_it1.188
r_angle_other_deg0.912
r_mcbond_it0.638
r_symmetry_vdw_other0.245
r_nbd_other0.222
r_nbd_refined0.219
r_xyhbond_nbd_refined0.212
r_symmetry_hbond_refined0.164
r_symmetry_vdw_refined0.159
r_nbtor_other0.086
r_chiral_restr0.08
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4169
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing