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Crystal Structure of Spin-Labeled T77C TNFa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 TNFa (VCID10616, B114005) at 10 mg/ml (in 10 mM HEPES, pH = 7.5, 150 mM NaCl) was mixed with an equal volume of protein solution and a solution containing 24% (w/v) PEG-4000, 0.24 M MgCl2, 0.05% DDM, and 0.1 M HEPES/NaOH, pH=8.5. Crystals were produced by sitting drop vapor diffusion at 16 degrees Celsius. Crystals were then soaked with the same solution supplemented with 10% MTSL for one week and harvested with paraffin oil.
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.66 α = 90 b = 65.66 β = 90 c = 84.09 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 MARMOSAIC 225 mm CCD 2016-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 32.83 98 0.074 0.997 12.71 3.78 26091 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 91.8 0.572 0.608 3.02
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 1tnf 1.4 32.83 1.97 26091 2115 97.96 0.1478 0.1393 0.1396 0.17 0.168
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 18.184 f_angle_d 1.274 f_chiral_restr 0.093 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1018 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing