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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 7 293 0.1 M HEPES pH 7
PEG 400 35%
Crystal Properties Matthews coefficient Solvent content 2.76 55.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.566 α = 90 b = 65.973 β = 90 c = 86.904 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 PILATUS3 6M 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.12 65.97 100 0.102 0.116 0.044 0.996 7.4 6.8 15149 45.69
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 2.12 2.16 1.234 0.584 0.64
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1Q3O 2.12 43.45 1.34 15065 709 99.74 0.216 0.2145 0.2462 0.2717 54.81
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 13.6961 f_angle_d 0.8949 f_chiral_restr 0.0565 f_bond_d 0.008 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1610 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data processing Aimless data scaling pointless data scaling PHASER phasing Coot model building DIALS data reduction