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1.4 A RESOLUTION STRUCTURE OF MOUSE TUMOR NECROSIS FACTOR, TOWARDS MODULATION OF ITS SELECTIVITY AND TRIMERISATION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TNF PDB ENTRY 1TNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 EQUAL VOLUMES OF RESERVOIR SOLUTION, CONTAINING 7 % ISOPROP, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.214 α = 114.81 b = 48.3 β = 103.65 c = 51.095 γ = 91.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH RHODIUM COATED PRE-MIRROR, SEGMENTED MIRROR 1997-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.4 20 90.9 0.029 19 1.8 72552 15.1
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) 1.4 1.5 85.5 0.148 5.7 1.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TNF 1.4 8 2 67767 6871 85.8 0.201 0.201 0.1974 0.235 RANDOM 19.7
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 x_dihedral_angle_d 27.3 x_scangle_it 2.99 x_mcangle_it 2.59 x_scbond_it 1.98 x_angle_deg 1.6 x_mcbond_it 1.48 x_improper_angle_d 1.39 x_bond_d 0.01 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 27.3 x_scangle_it 2.99 x_mcangle_it 2.59 x_scbond_it 1.98 x_angle_deg 1.6 x_mcbond_it 1.48 x_improper_angle_d 1.39 x_bond_d 0.01 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3477 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building X-PLOR refinement X-PLOR phasing