☰ Navigation Tabs
Crystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7.5 277 10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 5 mM DTT, 200 uM ADP, 200 uM aluminum nitrate, 1.2 mM sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.251 α = 90 b = 82.251 β = 90 c = 280.354 γ = 120
Symmetry Space Group P 61 2 2
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 PSI PILATUS 6M 2015-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98401 SSRL BL12-2
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 2.5 39.07 97 0.233 0.263 0.118 0.986 4.8 4.4 19517 54.32
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 2.5 2.6 98.9 2.733 2.935 1.388 0.188 0.5 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4NM7 2.5 39.07 1.33 19434 939 95.34 0.2101 0.2091 0.2106 0.2506 0.2509 68.34
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.3048 f_angle_d 0.5394 f_chiral_restr 0.0417 f_plane_restr 0.0045 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2973 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 52
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction pointless data scaling Aimless data scaling PHENIX phasing PHENIX refinement Coot model building