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Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide
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 293 100 nL of protein solution (15 mg/ml mutant protein in 10 mM HEPES buffer, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP) were mixed with 100 nL reservoir buffer (16% (w/v) polyethylene glycol 3350 and 0.2 M ammonium citrate), above a reservoir volume of 20 microL
Crystal Properties Matthews coefficient Solvent content 3.01 59.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.799 α = 90 b = 67.799 β = 90 c = 248.967 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER X 16M 2019-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 47.932 100 0.999 12.2 9.2 24047 31.7924470837
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.6 0.78 2.2 9.5
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 2 47.9319903751 1.34056753806 23944 1209 99.887363898 0.203122312625 0.200578430683 0.2026 0.249057148164 0.2514 44.1341826172
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 16.6665662376 f_angle_d 0.760141956248 f_chiral_restr 0.0496298246419 f_plane_restr 0.00612171623386 f_bond_d 0.00609183812312
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing