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Apo PDZ domain from mouse SHANK3 (570-664)
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, HANGING DROP 6 292.15 100 mM Bis-tris pH 6.0, 1.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.516 α = 90 b = 33.808 β = 90 c = 107.504 γ = 90
Symmetry Space Group I 1 2 1
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 PILATUS3 6M 2026-02-06 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) R Merge I (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 1.26 53.74 99.7 0.082 0.052 1 7.5 3.3 26856 13.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 1.433 1.961 0.296
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 1.261 53.74 26849 1325 99.929 0.151 0.1494 0.1498 0.1777 0.1557 20.571
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] -0.679 -0.117 -0.823 1.501
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.215 r_dihedral_angle_6_deg 17.376 r_lrange_other 17.37 r_dihedral_angle_3_deg 11.472 r_scangle_it 11.119 r_scangle_other 11.11 r_mcangle_other 9.052 r_mcangle_it 9.01 r_scbond_it 7.863 r_scbond_other 7.857
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.215 r_dihedral_angle_6_deg 17.376 r_lrange_other 17.37 r_dihedral_angle_3_deg 11.472 r_scangle_it 11.119 r_scangle_other 11.11 r_mcangle_other 9.052 r_mcangle_it 9.01 r_scbond_it 7.863 r_scbond_other 7.857 r_dihedral_angle_1_deg 6.982 r_mcbond_it 6.434 r_mcbond_other 6.195 r_dihedral_angle_2_deg 5.353 r_rigid_bond_restr 4.62 r_angle_refined_deg 2.073 r_angle_other_deg 0.673 r_nbd_refined 0.198 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.192 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.156 r_chiral_restr 0.1 r_symmetry_xyhbond_nbd_other 0.096 r_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 763 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing