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Crystal structure of Human Catenin Beta-1 in complex with cyclic beta sheet peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 277.15 100 mM Tris pH 8.25 0-10 %(w/v) PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.869 α = 90 b = 103.584 β = 90 c = 187.532 γ = 90
Symmetry Space Group C 2 2 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 2025-04-05 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 2.09 54.37 93.2 0.015 1 22.8 54.6 31898
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 2.09 2.23 45.5 0.227 0.84 1.3 57.5
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 THROUGHOUT 2.094 54.37 31893 1608 86.109 0.19 0.1882 0.1972 0.2171 0.2263 RANDOM 60.233
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] -0.864 0.263 0.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.499 r_dihedral_angle_6_deg 9.676 r_lrange_other 9.315 r_lrange_it 9.31 r_scangle_it 7.495 r_scangle_other 7.494 r_mcangle_it 5.135 r_mcangle_other 5.126 r_scbond_it 4.807 r_scbond_other 4.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.499 r_dihedral_angle_6_deg 9.676 r_lrange_other 9.315 r_lrange_it 9.31 r_scangle_it 7.495 r_scangle_other 7.494 r_mcangle_it 5.135 r_mcangle_other 5.126 r_scbond_it 4.807 r_scbond_other 4.806 r_dihedral_angle_1_deg 4.753 r_mcbond_it 3.598 r_mcbond_other 3.592 r_dihedral_angle_2_deg 2.059 r_angle_refined_deg 0.763 r_angle_other_deg 0.301 r_nbd_refined 0.193 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.112 r_nbd_other 0.099 r_symmetry_nbtor_other 0.065 r_symmetry_nbd_refined 0.063 r_symmetry_xyhbond_nbd_refined 0.043 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3985 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement GDA data collection xia2.multiplex data reduction STARANISO data scaling PHASER phasing