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SHANK3 PDZ (570-664) in complex with an internal PDZ binding motif (843-864) in Densin-180
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292.15 60 mM magnesium chloride hexahydrate, 60 mM calcium chloride dihydrate, 100 mM Tris/Bicine pH 8.5, 12% v/v PEG 500 MME, 6% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.89 α = 90 b = 71.34 β = 90 c = 114.92 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 X 9M 2026-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.62 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.98 47.64 100 0.201 1 7.6 6.6 37309
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 99.8 1.804 0.4 1.1 5.7
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 1.98 47.639 37260 1727 99.89 0.204 0.201 0.2042 0.2566 0.2066 39.889
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] -1.55 1.401 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.622 r_dihedral_angle_6_deg 15.499 r_lrange_it 9.291 r_lrange_other 9.272 r_dihedral_angle_2_deg 8.428 r_dihedral_angle_1_deg 6.644 r_scangle_it 6.543 r_scangle_other 6.542 r_mcangle_it 5.913 r_mcangle_other 5.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.622 r_dihedral_angle_6_deg 15.499 r_lrange_it 9.291 r_lrange_other 9.272 r_dihedral_angle_2_deg 8.428 r_dihedral_angle_1_deg 6.644 r_scangle_it 6.543 r_scangle_other 6.542 r_mcangle_it 5.913 r_mcangle_other 5.912 r_scbond_it 4.322 r_scbond_other 4.32 r_mcbond_it 4.011 r_mcbond_other 4.01 r_angle_refined_deg 1.728 r_angle_other_deg 0.581 r_symmetry_nbd_refined 0.217 r_nbd_other 0.208 r_nbd_refined 0.206 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3524 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing