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Crystal Structure of Scribble PDZ34 tandem in complex with its target peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 10% (w/v) PEG 3350, 0.2M KI, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.97 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.27 α = 90 b = 78.43 β = 99.51 c = 94.08 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2013-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 98.1 0.121 0.27 0.133 8.8 4.7 18220 18220 38.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.5 0.505 0.618 0.343 3.4 4.8 1844
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 4WYT 2.5 36.758 1.34 18176 903 97.77 0.1908 0.1889 0.1928 0.2274 0.2293 46.9846
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 12.836 f_angle_d 0.813 f_chiral_restr 0.032 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3081 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement iMOSFLM data processing PHASER phasing PDB_EXTRACT data extraction SCALA data scaling