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Beta-catenin armadillo with cyclic peptide and Compound 2
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, SITTING DROP 293 0.1 M Bis-TRIS pH 6.5, 0.2 M Lithium sulfate monohydrate, 26% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.56 α = 90 b = 90.94 β = 90 c = 120.34 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 S 16M 2021-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03319 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.98 47.4 97.1 0.998 6.69 7.94 39292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.1 0.014
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 45.47 36753 1935 99.25 0.22147 0.21805 0.2229 0.28596 0.289 RANDOM 59.084
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] -2.04 -2.12 4.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.864 r_long_range_B_refined 11.435 r_long_range_B_other 11.434 r_dihedral_angle_2_deg 11.167 r_scangle_other 9.57 r_scbond_it 6.805 r_scbond_other 6.639 r_mcangle_it 6.112 r_mcangle_other 6.111 r_dihedral_angle_1_deg 5.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.864 r_long_range_B_refined 11.435 r_long_range_B_other 11.434 r_dihedral_angle_2_deg 11.167 r_scangle_other 9.57 r_scbond_it 6.805 r_scbond_other 6.639 r_mcangle_it 6.112 r_mcangle_other 6.111 r_dihedral_angle_1_deg 5.913 r_mcbond_it 4.665 r_mcbond_other 4.664 r_angle_refined_deg 1.49 r_angle_other_deg 0.491 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4015 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing