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Crystal structure of imidazo quinoxaline 1 bound to the kinase domain of human LCK, activated form (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% PEG8000, 5.2% MPD, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.591 α = 90 b = 73.807 β = 90 c = 92.159 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 2002-11-10 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) 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 2.7 28.44 99.5 0.13 10.2 3.4 7521 8411 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.85 100 0.246 5.3 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LCK 2.7 15 7521 811 99.52 0.18583 0.17607 0.1774 0.27447 0.2762 RANDOM 5.23
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] -1.22 0.32 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.991 r_dihedral_angle_4_deg 25.623 r_dihedral_angle_3_deg 19.524 r_dihedral_angle_1_deg 7.465 r_scangle_it 2.792 r_angle_refined_deg 2.265 r_scbond_it 1.723 r_mcangle_it 1.1 r_mcbond_it 0.633 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.991 r_dihedral_angle_4_deg 25.623 r_dihedral_angle_3_deg 19.524 r_dihedral_angle_1_deg 7.465 r_scangle_it 2.792 r_angle_refined_deg 2.265 r_scbond_it 1.723 r_mcangle_it 1.1 r_mcbond_it 0.633 r_nbtor_refined 0.323 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.137 r_bond_refined_d 0.024 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement BSS data collection MOSFLM data reduction SCALA data scaling AMoRE phasing