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Crystal structure of beta-catenin in complex with cyclic peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.1 M HEPES, 4% PEG6000, 20 mM TRIS, 150 mM NaCl, 0.5 % Glycerol, 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.62 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.38 α = 90 b = 85.62 β = 90 c = 142.71 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 100 PIXEL DECTRIS EIGER2 X 16M 2020-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979507 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.6 85.62 100 0.171 0.999 12.83 13.36 27652
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 100 3 0.584 1.11 14.23
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JDH 2.6 85.62 27596 1380 99.975 0.205 0.2026 0.2419 0.2337 72.408
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] -1.05 1.54 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.326 r_dihedral_angle_4_deg 17.936 r_dihedral_angle_3_deg 15.973 r_dihedral_angle_1_deg 5.635 r_lrange_other 4.466 r_lrange_it 4.463 r_scangle_it 2.406 r_scangle_other 2.405 r_mcangle_it 2.201 r_mcangle_other 2.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.326 r_dihedral_angle_4_deg 17.936 r_dihedral_angle_3_deg 15.973 r_dihedral_angle_1_deg 5.635 r_lrange_other 4.466 r_lrange_it 4.463 r_scangle_it 2.406 r_scangle_other 2.405 r_mcangle_it 2.201 r_mcangle_other 2.181 r_angle_refined_deg 1.423 r_scbond_it 1.416 r_scbond_other 1.416 r_mcbond_it 1.312 r_mcbond_other 1.312 r_angle_other_deg 1.224 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.203 r_nbd_other 0.201 r_symmetry_nbd_other 0.174 r_symmetry_nbd_refined 0.165 r_xyhbond_nbd_refined 0.152 r_nbtor_refined 0.147 r_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4017 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing