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Dishevelled 2 PDZ domain in complex with Daple 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 NaAcetate, pH 4.6, 3% MPD
Crystal Properties Matthews coefficient Solvent content 1.74 29.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.664 α = 90 b = 52.762 β = 90 c = 65.475 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 EIGER X 16M 2021-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.00 Diamond I24
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 1.4 43.2 99.8 0.104 0.112 39.2 14.9 62886
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 1.4 1.48 1.18 1.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 41.083 33210 1646 99.742 0.175 0.1733 0.1812 0.207 0.2175 17.974
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] -0.904 -0.28 1.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.323 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_1_deg 7.083 r_lrange_it 7.022 r_lrange_other 6.993 r_dihedral_angle_2_deg 5.874 r_scangle_it 4.115 r_scangle_other 4.114 r_mcangle_it 3.468 r_mcangle_other 3.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.323 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_1_deg 7.083 r_lrange_it 7.022 r_lrange_other 6.993 r_dihedral_angle_2_deg 5.874 r_scangle_it 4.115 r_scangle_other 4.114 r_mcangle_it 3.468 r_mcangle_other 3.468 r_scbond_it 2.747 r_scbond_other 2.745 r_mcbond_it 2.165 r_mcbond_other 2.164 r_angle_refined_deg 1.597 r_angle_other_deg 0.548 r_nbd_refined 0.224 r_nbd_other 0.202 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1649 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing