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asymmetric mTNF-alpha hTNFR1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 2.0M Ammonium sulfate, 0.1M BisTris pH5.5, and cryo-protected with paraffin oil; Vapor diffusion, sitting drop, temperature 289K.
Crystal Properties Matthews coefficient Solvent content 3.98 69.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.22 α = 90 b = 139.22 β = 90 c = 138.34 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 2014-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.65 50 99.5 0.065 19.98 3.7 43935 49.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.72 99.5 0.545 2.83 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished structure 2.65 49.07 43935 2045 99.47 0.195 0.193 0.227 0.1749 RANDOM 48.464
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] 0.45 0.22 0.45 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_4_deg 22.852 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 6.562 r_mcangle_it 4.96 r_mcbond_it 3.2 r_mcbond_other 3.2 r_angle_refined_deg 1.426 r_angle_other_deg 0.941 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_4_deg 22.852 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 6.562 r_mcangle_it 4.96 r_mcbond_it 3.2 r_mcbond_other 3.2 r_angle_refined_deg 1.426 r_angle_other_deg 0.941 r_chiral_restr 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6486 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 225
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing