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Crystal structure of Triazolone derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LCK PDB ENTRY 3LCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2M (NH4)2SO4, 0.1M SODIUM CACODYLATE, 30% PEG 8000, 0.2% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.961 α = 90 b = 73.61 β = 90 c = 91.96 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU JUPITER 210 2002-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0 SPring-8 BL32B2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 41.96 100 0.059 0.064 25.7 7.1 19902 19948 18.6
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) Redundancy Number Unique Reflections (All) 2 2.11 100 0.128 0.137 14.3 7.3 2872
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LCK 2 10 17695 2010 99.97 0.16081 0.1543 0.21845 0.2057 RANDOM 14.811
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] -0.38 0.02 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.346 r_dihedral_angle_4_deg 15.569 r_dihedral_angle_3_deg 13.788 r_scangle_it 5.848 r_dihedral_angle_1_deg 5.65 r_scbond_it 3.88 r_mcangle_it 2.387 r_mcbond_it 1.485 r_angle_refined_deg 1.377 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.346 r_dihedral_angle_4_deg 15.569 r_dihedral_angle_3_deg 13.788 r_scangle_it 5.848 r_dihedral_angle_1_deg 5.65 r_scbond_it 3.88 r_mcangle_it 2.387 r_mcbond_it 1.485 r_angle_refined_deg 1.377 r_chiral_restr 0.086 r_gen_planes_refined 0.015 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2212 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 53
Software Software Software Name Purpose BSS data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling