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Crystal Structure of Methoxy Benzofuran 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 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.277 α = 90 b = 73.612 β = 90 c = 92.76 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 2002-11-01 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 28.5 95.4 0.107 0.124 12.5 3.7 14486 14511 15.9
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 92.2 0.213 0.245 7.3 3.9 2007
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 12854 1456 94.8 0.17738 0.16852 0.175 0.25551 0.2586 RANDOM 20.559
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] -0.41 0.45 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.609 r_dihedral_angle_3_deg 15.202 r_dihedral_angle_4_deg 15.137 r_dihedral_angle_1_deg 6.604 r_scangle_it 4.094 r_scbond_it 2.634 r_angle_refined_deg 1.768 r_mcangle_it 1.614 r_mcbond_it 0.887 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.609 r_dihedral_angle_3_deg 15.202 r_dihedral_angle_4_deg 15.137 r_dihedral_angle_1_deg 6.604 r_scangle_it 4.094 r_scbond_it 2.634 r_angle_refined_deg 1.768 r_mcangle_it 1.614 r_mcbond_it 0.887 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2210 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 41
Software Software Software Name Purpose BSS data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling