☰ Navigation Tabs
Crystal structure of Human Catenin Beta-1 in complex with linear 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 277.15 100 mM Tris pH 8.25, 12 %(v/v) PEG-3350; 100 mM Tris pH 9, 8 %(v/v) PEG-6000
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.91 α = 90 b = 103.962 β = 90 c = 186.705 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 2024-10-09 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 2.33 54.504 92.6 0.039 1 9.9 53.9 20764
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 2.33 2.5 54.3 0.543 0.49 0.6 54.6
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 2.33 54.504 20761 1042 76.87 0.212 0.2088 0.2183 0.2663 0.2687 RANDOM 68.895
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] 1.341 -1.792 0.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.832 r_dihedral_angle_6_deg 12.761 r_lrange_other 10.02 r_lrange_it 10.019 r_scangle_it 5.407 r_scangle_other 5.406 r_dihedral_angle_1_deg 5.325 r_dihedral_angle_2_deg 4.756 r_mcangle_it 4.685 r_mcangle_other 4.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.832 r_dihedral_angle_6_deg 12.761 r_lrange_other 10.02 r_lrange_it 10.019 r_scangle_it 5.407 r_scangle_other 5.406 r_dihedral_angle_1_deg 5.325 r_dihedral_angle_2_deg 4.756 r_mcangle_it 4.685 r_mcangle_other 4.685 r_scbond_it 3.241 r_scbond_other 3.24 r_mcbond_it 2.913 r_mcbond_other 2.91 r_angle_refined_deg 1.137 r_angle_other_deg 0.393 r_symmetry_xyhbond_nbd_other 0.229 r_nbd_refined 0.221 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.172 r_nbd_other 0.141 r_symmetry_nbd_refined 0.12 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3953 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement GDA data collection DIALS data reduction STARANISO data scaling PHASER phasing