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Crystal structure of beta-catenin in complex with alpha-helical peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 300 Crystals grown in 100 mM NaKPO4, 2M NaCl.
Crystal Properties Matthews coefficient Solvent content 2.03 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.526 α = 90 b = 91.255 β = 90 c = 112.984 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 XE 16M 2023-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.001 71.013 93.5 0.03 1 11.6 52 18536 1 36.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.002 2.207 61.8 0.124 0.958 1.2 30.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.001 70.991 18535 935 52.451 0.186 0.1839 0.1924 0.2317 0.2387 RANDOM 41.859
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] 0.276 0.34 -0.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.556 r_dihedral_angle_3_deg 10.941 r_lrange_it 8.363 r_lrange_other 8.363 r_scangle_it 6.285 r_scangle_other 6.284 r_dihedral_angle_1_deg 4.419 r_mcangle_it 4.034 r_mcangle_other 4.027 r_dihedral_angle_2_deg 3.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.556 r_dihedral_angle_3_deg 10.941 r_lrange_it 8.363 r_lrange_other 8.363 r_scangle_it 6.285 r_scangle_other 6.284 r_dihedral_angle_1_deg 4.419 r_mcangle_it 4.034 r_mcangle_other 4.027 r_dihedral_angle_2_deg 3.989 r_scbond_it 3.985 r_scbond_other 3.984 r_mcbond_it 2.687 r_mcbond_other 2.682 r_angle_refined_deg 0.921 r_angle_other_deg 0.286 r_nbd_refined 0.19 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.158 r_nbd_other 0.15 r_symmetry_nbd_refined 0.137 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.037 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3976 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing STARANISO data scaling xia2.multiplex data reduction GDA data collection