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Dishevelled 2 PDZ domain in complex with Frizzled 4 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Mg Formate, 15% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.987 α = 90 b = 88.062 β = 90 c = 108.644 γ = 90
Symmetry Space Group I 2 2 2
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 EIGER X 16M 2018-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 50 99.9 0.026 0.029 39.2 12.9 30950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.79 1.57 1.88
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 44.07 30839 1504 99.922 0.258 0.2562 0.2607 0.285 0.2905 50.205
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] 0.779 -1.985 1.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.453 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_1_deg 7.698 r_lrange_it 6.36 r_lrange_other 6.359 r_dihedral_angle_2_deg 5.401 r_scangle_it 4.306 r_scangle_other 4.304 r_mcangle_it 3.253 r_mcangle_other 3.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.453 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_1_deg 7.698 r_lrange_it 6.36 r_lrange_other 6.359 r_dihedral_angle_2_deg 5.401 r_scangle_it 4.306 r_scangle_other 4.304 r_mcangle_it 3.253 r_mcangle_other 3.252 r_scbond_it 2.751 r_scbond_other 2.749 r_mcbond_it 2.303 r_mcbond_other 2.303 r_angle_refined_deg 1.581 r_angle_other_deg 0.517 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_refined 0.203 r_symmetry_nbd_other 0.196 r_nbd_other 0.173 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.131 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2088 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing