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Leishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7S6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 PEG3350 20%, 300 mM Li2SO4, 100 mM SBG (42.8 mM Sodium tartrate dihydrate, 28.6 mM Bis-Tris and 28.6 mM Glycylglycine)
Crystal Properties Matthews coefficient Solvent content 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.163 α = 90 b = 39.871 β = 101.09 c = 62.801 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.66 76.62 98.6 0.058 0.063 0.025 0.999 15.8 6.1 44340
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 0.793 0.873 0.356 0.695 2.1
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 7S6U 1.66 76.62 42220 2120 98.48 0.1854 0.1839 0.1969 0.2154 0.2264 RANDOM 26.431
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] 1.02 -0.58 -1.16 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.559 r_dihedral_angle_4_deg 21.524 r_dihedral_angle_3_deg 13.06 r_dihedral_angle_1_deg 7.118 r_angle_refined_deg 1.935 r_angle_other_deg 1.542 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.559 r_dihedral_angle_4_deg 21.524 r_dihedral_angle_3_deg 13.06 r_dihedral_angle_1_deg 7.118 r_angle_refined_deg 1.935 r_angle_other_deg 1.542 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2681 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing