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Crystal structure of phenylimidazo pyrazin 2 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% PEG8000, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.15 α = 90 b = 73.973 β = 90 c = 92.857 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 2003-01-01 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 2.55 28.51 98.5 0.101 0.12 11.8 3.3 9817 9965 26.7
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) 2.55 2.69 96.6 0.211 0.248 5.9 3.4 1372
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 2.55 15 8763 968 98.3 0.18336 0.17145 0.1735 0.29127 0.2924 RANDOM 8.431
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] 0.04 0.48 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.147 r_dihedral_angle_4_deg 21.433 r_dihedral_angle_3_deg 19.395 r_dihedral_angle_1_deg 8.825 r_scangle_it 6.602 r_scbond_it 4.969 r_mcangle_it 3.324 r_mcbond_it 2.315 r_angle_refined_deg 1.662 r_symmetry_hbond_refined 0.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.147 r_dihedral_angle_4_deg 21.433 r_dihedral_angle_3_deg 19.395 r_dihedral_angle_1_deg 8.825 r_scangle_it 6.602 r_scbond_it 4.969 r_mcangle_it 3.324 r_mcbond_it 2.315 r_angle_refined_deg 1.662 r_symmetry_hbond_refined 0.549 r_nbtor_refined 0.335 r_symmetry_vdw_refined 0.302 r_nbd_refined 0.275 r_xyhbond_nbd_refined 0.229 r_chiral_restr 0.138 r_gen_planes_refined 0.028 r_bond_refined_d 0.02
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement BSS data collection MOSFLM data reduction SCALA data scaling AMoRE phasing