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Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal structure of the antagonist-TNFalpha complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TNF PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4) experimental model PDB 1TN3 PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris, 0.35M MgAc, 20% 2-propanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.905 α = 90 b = 83.905 β = 90 c = 149.172 γ = 120
Symmetry Space Group P 63 2 2
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 MARRESEARCH M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.81500 EMBL/DESY, HAMBURG X12 2 SYNCHROTRON MAX II BEAMLINE I911-3 1.0 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 74 99.86 17880 17855 3 3
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 PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4) 2.1 41.95 17855 968 99.86 0.175 0.173 0.217 0.1924 RANDOM 29.367
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] 0.29 0.15 0.29 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.431 r_dihedral_angle_4_deg 18.222 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 6.42 r_scangle_it 4.718 r_scbond_it 2.915 r_mcangle_it 1.977 r_angle_refined_deg 1.475 r_mcbond_it 1.129 r_symmetry_hbond_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.431 r_dihedral_angle_4_deg 18.222 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 6.42 r_scangle_it 4.718 r_scbond_it 2.915 r_mcangle_it 1.977 r_angle_refined_deg 1.475 r_mcbond_it 1.129 r_symmetry_hbond_refined 0.319 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.11 r_metal_ion_refined 0.045 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2206 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing