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Crystal structure of SHANK1 PDZ in complex with a SLiM internal ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20 % v/v ethylene glycol, 10 % w/v PEG 8000, 0.018 M magnesium chloride, 0.018 M calcium chloride, 0.1 M tris pH 7.5, 0.1 M bicine pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.01 69.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.101 α = 90 b = 149.101 β = 90 c = 64.066 γ = 120
Symmetry Space Group P 32 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 EIGER2 X CdTe 9M 2022-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 1.979 129.125 100 0.123 0.039 0.999 14.7 20.7 57199 34.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.979 2.01 1.661 0.56 0.837 1.2
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 1.979 129.125 57178 3012 100 0.217 0.2158 0.2157 0.2358 0.2363 46.681
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] 0.787 0.393 0.787 -2.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_3_deg 13.313 r_dihedral_angle_4_deg 12.086 r_lrange_other 8.826 r_lrange_it 8.822 r_dihedral_angle_1_deg 6.681 r_scangle_it 6.273 r_scangle_other 6.273 r_mcangle_it 5.179 r_mcangle_other 5.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_3_deg 13.313 r_dihedral_angle_4_deg 12.086 r_lrange_other 8.826 r_lrange_it 8.822 r_dihedral_angle_1_deg 6.681 r_scangle_it 6.273 r_scangle_other 6.273 r_mcangle_it 5.179 r_mcangle_other 5.178 r_scbond_it 3.949 r_scbond_other 3.949 r_mcbond_it 3.426 r_mcbond_other 3.426 r_angle_refined_deg 1.399 r_angle_other_deg 1.236 r_symmetry_xyhbond_nbd_refined 0.239 r_nbd_refined 0.184 r_symmetry_nbd_other 0.165 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.163 r_nbtor_refined 0.153 r_symmetry_nbd_refined 0.105 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3596 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 12
Software Software Software Name Purpose DIALS data reduction PHASER phasing Coot model building REFMAC refinement