6PDJ

Tyrosine-protein kinase LCK bound to Compound 11


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP10.52911.5 M ammonium sulfate, 120 mM lithium chloride, 10 mM nickel(II) chloride, 100 mM CAPS pH 10.5
Crystal Properties
Matthew coefficientSolvent content
2.4449.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.016α = 90
b = 74.163β = 90
c = 104.527γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKirkpatrick-Baez mirrors2015-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.8138.98489.80.0669.76.4613665621.04
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.9750.464

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 REPLACEMENTTHROUGHOUT1QPJ1.8126.1321199103969.60.1690.1670.217RANDOM27.25
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]
1.961-0.7288-1.2322
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.28
t_omega_torsion3.57
t_angle_deg1.06
t_bond_d0.01
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.28
t_omega_torsion3.57
t_angle_deg1.06
t_bond_d0.01
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_trig_c_planes
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
t_dihedral_angle_d
t_gen_planes
t_it
t_sum_occupancies
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2178
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms59

Software

Software
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AutoPROCdata scaling
PHASERphasing