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Human TNFa dimer in complex with the semi-synthetic bicyclic peptide M21
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 6.5 293 25.5% PEG 8000, 0.085 M Na Cacodylate pH 6.5, 0.17M Ammonium Sulfate, 15% Glycerol.
Crystal Properties Matthews coefficient Solvent content 2.84 56.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.444 α = 90 b = 78.444 β = 90 c = 230.375 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2013-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.98 Diamond I04-1
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 2.85 46.08 99 0.144 9.1 7.7 19797
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 2.85 3.02 99.1 1.247 2 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 1TNF 2.85 76.79 18737 1005 98.65 0.22887 0.22593 0.28601 0.2775 RANDOM 81.851
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] 0.31 0.15 0.31 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.507 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 17.151 r_long_range_B_refined 14.881 r_long_range_B_other 14.881 r_mcangle_it 9.173 r_mcangle_other 9.171 r_scangle_other 8.722 r_dihedral_angle_1_deg 6.892 r_mcbond_it 5.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.507 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 17.151 r_long_range_B_refined 14.881 r_long_range_B_other 14.881 r_mcangle_it 9.173 r_mcangle_other 9.171 r_scangle_other 8.722 r_dihedral_angle_1_deg 6.892 r_mcbond_it 5.801 r_mcbond_other 5.801 r_scbond_it 5.701 r_scbond_other 5.693 r_angle_other_deg 2.596 r_angle_refined_deg 1.692 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4533 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing Coot model building