4O2P | pdb_00004o2p

Kinase domain of cSrc in complex with a substituted pyrazolopyrimidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OIQPDB ENTRY 2OIQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729310% ETHYLENE GLYCOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.215α = 101.35
b = 63.248β = 90.44
c = 74.813γ = 90.07
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELPSI PILATUS 6MDYNAMIC BENDABLE MIRROR2011-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.978600SLSX10SA

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
12.15096.10.04411.851.924425242544-336.53
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)
12.12.295.40.2013.951.955497

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OIQ2.143.34442524254485196.110.19740.19660.20.23850.24RANDOM37.379
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]
-0.140.090.160.09-0.77-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.817
r_dihedral_angle_4_deg14.412
r_dihedral_angle_3_deg14.192
r_dihedral_angle_1_deg5.528
r_angle_refined_deg1.142
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.817
r_dihedral_angle_4_deg14.412
r_dihedral_angle_3_deg14.192
r_dihedral_angle_1_deg5.528
r_angle_refined_deg1.142
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms4241
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms68

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XSCALEdata scaling