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Trimeric crystal structure of vimentin coil1B fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SWK 3SWK, 3UF1 experimental model PDB 3UF1 3SWK, 3UF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 298 protein in 10 mM Tris pH 8, 38 mM NaCl mixed in ratio 1:1 with 1M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.447 α = 90 b = 35.447 β = 90 c = 200.08 γ = 120
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 2010-11-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97926 SOLEIL PROXIMA 1 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.8856 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim 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 1.44 20 99.7 0.069 0.069 0.073 19.94 10.46 16952 16952 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.48 99.7 0.567 0.658 2.32 3.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FREE R-VALUE 3SWK, 3UF1 1.44 19.39 16948 853 99.74 0.2533 0.2477 0.2497 0.2764 0.2725 PHENIX selection 24.0127
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 14.546 f_angle_d 0.94 f_chiral_restr 0.069 f_bond_d 0.007 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 694 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction