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Crystal structure of imidazo pyrimidine 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 2.18 43.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.233 α = 90 b = 73.671 β = 90 c = 92.719 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 2002-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.5418 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 2.2 28.75 96.7 0.123 0.148 10.3 3.1 14684 14715 20.7
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) 2.2 2.32 98 0.219 0.26 6 3.4 2147
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 2.2 10 13067 1485 96.47 0.17512 0.16698 0.1735 0.2471 0.2489 RANDOM 25.576
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] -0.8 0.82 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.956 r_dihedral_angle_3_deg 14.254 r_dihedral_angle_4_deg 14.147 r_dihedral_angle_1_deg 5.899 r_scangle_it 4.861 r_scbond_it 3.197 r_mcangle_it 1.974 r_angle_refined_deg 1.356 r_mcbond_it 1.18 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.956 r_dihedral_angle_3_deg 14.254 r_dihedral_angle_4_deg 14.147 r_dihedral_angle_1_deg 5.899 r_scangle_it 4.861 r_scbond_it 3.197 r_mcangle_it 1.974 r_angle_refined_deg 1.356 r_mcbond_it 1.18 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2210 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 36
Software Software Software Name Purpose BSS data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling