3DQX

chicken c-Src kinase domain in complex with ATPgS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529310% PEG 4000, 50 mM Ammonium acetate, 100 mM Bis-Tris pH 5.5, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.507α = 90
b = 119.15β = 90.36
c = 63.676γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.35096.60.0620.062183.62716427164
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3881.40.2050.2054.493

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2SRC with deletion of residues 300-315 and 400-4252.334.612576625766137096.390.193850.191230.24131RANDOM53.856
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]
0.3-0.1-0.22-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.023
r_dihedral_angle_3_deg17.894
r_dihedral_angle_4_deg15.686
r_dihedral_angle_1_deg5.746
r_scangle_it2.592
r_scbond_it1.648
r_angle_refined_deg1.263
r_mcangle_it0.917
r_mcbond_it0.481
r_symmetry_hbond_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.023
r_dihedral_angle_3_deg17.894
r_dihedral_angle_4_deg15.686
r_dihedral_angle_1_deg5.746
r_scangle_it2.592
r_scbond_it1.648
r_angle_refined_deg1.263
r_mcangle_it0.917
r_mcbond_it0.481
r_symmetry_hbond_refined0.311
r_nbtor_refined0.301
r_symmetry_vdw_refined0.202
r_nbd_refined0.183
r_xyhbond_nbd_refined0.139
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4299
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing