☰ Navigation Tabs
Crystal Structure of Canine TNF-alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.6 M MgSO4, 100 mM MES, pH 5.6.
Crystal Properties Matthews coefficient Solvent content 2.04 39.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.119 α = 90 b = 67.119 β = 90 c = 79.024 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 98 CCD RAYONIX MX300HE 2022-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 18 99.4 0.03 0.98 44.9 4.7 11257 15.9585259751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 100 0.242 0.96 5.9 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85016596237 16.77975 1.99610631886 11257 598 99.4083362769 0.170531742474 0.16826326764 0.1685 0.214920291661 0.2126 24.7522334178
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 8.00080125573 f_angle_d 0.999152948791 f_chiral_restr 0.0613873775527 f_bond_d 0.00840502968838 f_plane_restr 0.00648584587226
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1154 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection HKL-3000 data scaling REFMAC phasing Coot model building PHENIX refinement HKL-3000 data reduction