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Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES 7.75
PEG 400 40%
30% w/v Trimethylamine N-oxide dihydrate
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.668 α = 90 b = 65.912 β = 90 c = 85.637 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 PILATUS 2M 2019-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.708 52.232 81.88 0.05 0.015 1 19.1 12.3 23326 33.77
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 1.708 1.808 1.838 0.612 0.706 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1Q3O 1.8 52.23 1.34 22226 1914 92.17 0.225 0.2222 0.2323 0.2551 0.2597 44.99
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.8415 f_angle_d 0.8834 f_chiral_restr 0.0587 f_bond_d 0.0082 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1614 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction STARANISO data scaling autoPROC data scaling PHASER phasing Coot model building XDS data reduction