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Crystal structure of imidazo pyrazin 1 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, 5.2% MPD, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.308 α = 90 b = 73.83 β = 90 c = 92.49 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 2003-02-13 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 2.1 28.44 98.9 0.087 13.8 3.4 15500 17341 9.251
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) 2.1 2.21 100 0.19 7.9 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 2.1 15 15500 1755 98.72 0.17209 0.16521 0.1674 0.23177 0.2338 RANDOM 6.285
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] 0.01 -0.24 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.638 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 6.628 r_scangle_it 3.047 r_scbond_it 2.021 r_angle_refined_deg 1.605 r_mcangle_it 1.209 r_mcbond_it 0.763 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.638 r_dihedral_angle_4_deg 16.026 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 6.628 r_scangle_it 3.047 r_scbond_it 2.021 r_angle_refined_deg 1.605 r_mcangle_it 1.209 r_mcbond_it 0.763 r_nbtor_refined 0.303 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.223 r_xyhbond_nbd_refined 0.214 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement BSS data collection MOSFLM data reduction SCALA data scaling AMoRE phasing