3AC5

Crystal structure of triazolo pyrimidine derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2M (NH4)2SO4, 0.1M SODIUM CACODYLATE, 30% PEG 8000, 0.2% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1943.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.303α = 90
b = 73.809β = 90
c = 92.603γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102002-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.5418SPring-8BL32B2

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
12.528.4899.20.0660.076184.1103991043727.4
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)
2.52.6499.80.1340.15210.74.31499

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3LCK2.5109219100598.970.171110.160860.2675RANDOM32.025
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]
-0.880.730.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.858
r_dihedral_angle_4_deg16.546
r_dihedral_angle_3_deg15.95
r_dihedral_angle_1_deg5.479
r_scangle_it4.556
r_scbond_it2.92
r_mcangle_it1.832
r_angle_refined_deg1.119
r_mcbond_it0.985
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.858
r_dihedral_angle_4_deg16.546
r_dihedral_angle_3_deg15.95
r_dihedral_angle_1_deg5.479
r_scangle_it4.556
r_scbond_it2.92
r_mcangle_it1.832
r_angle_refined_deg1.119
r_mcbond_it0.985
r_chiral_restr0.087
r_bond_refined_d0.008
r_gen_planes_refined0.006
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2210
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms52

Software

Software
Software NamePurpose
BSSdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling