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Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TNF PDB ENTRY 1TNF and PDB ENTRY 1T7V experimental model PDB 1T7V PDB ENTRY 1TNF and PDB ENTRY 1T7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 PEG 6000, sodium citrate, 0.2M NaBr, pH 5.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.18 61.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.656 α = 90 b = 170.295 β = 92.04 c = 122.002 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 325 mm CCD Rh coated flat mirror 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.0047 SSRL BL11-1
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 2.8 50 96.8 0.081 9.7 3.7 99161
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 2.8 2.9 81 0.472 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TNF and PDB ENTRY 1T7V 2.8 38.77 98697 98697 4965 96.8 0.2362 0.2362 0.2391 0.2658 0.2652 RANDOM 74.422
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] 28.9 -8.141 -12.367 -16.532
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.48 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.48 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21654 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 252
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction Web-Ice data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing