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Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (YPTSII) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SFJ PDB: 3SFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 40% (w/v) polyethylene glycol (PEG) 3350, 0.15 M potassium thiocyanate (KSCN), 0.1 M 2-ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.009 α = 79.62 b = 35.043 β = 87.61 c = 65.626 γ = 90
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 270 2011-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.8856 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 19.308 96.4 31186 30055 4.9 17.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 95.4 0.395 3.57 5196
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT omit peptide density PDB: 3SFJ 1.6 19.308 1.99 30050 1467 96.44 0.2069 0.2048 0.1974 0.2487 0.2397 In thin shells
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] -4.9851 0.2691 -0.9302 3.0359 1.8044 1.9492
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.961 f_angle_d 1.067 f_chiral_restr 0.067 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1837 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing