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The crystal structure of TNF family member EDA-A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other EDA-A1 trimer containing residues 248-307, 319-333, 347-390
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.2M NaCl, 0.1M Hepes, 25% Peg 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 19K
Crystal Properties Matthews coefficient Solvent content 1.9 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.723 α = 90 b = 161.337 β = 105.24 c = 51.023 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 IMAGE PLATE MARRESEARCH Osmic Mirrors 2003-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.23 30 96.8 0.03 0.043 23 2.7 38487 37259 -3 25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.33 94.6 0.089 9.5 2.51 3698
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 (All) 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 EDA-A1 trimer containing residues 248-307, 319-333, 347-390 2.23 30 37233 33523 3700 97.25 0.2043 0.2043 0.20009 0.202 0.24052 0.2414 THIN SHELLS 6.364
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] 0.26 0.55 -0.61 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.419 r_dihedral_angle_1_deg 6.762 r_scangle_it 2.644 r_mcangle_it 1.826 r_scbond_it 1.799 r_mcbond_it 1.189 r_angle_refined_deg 1.159 r_angle_other_deg 0.757 r_symmetry_vdw_refined 0.292 r_symmetry_vdw_other 0.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.419 r_dihedral_angle_1_deg 6.762 r_scangle_it 2.644 r_mcangle_it 1.826 r_scbond_it 1.799 r_mcbond_it 1.189 r_angle_refined_deg 1.159 r_angle_other_deg 0.757 r_symmetry_vdw_refined 0.292 r_symmetry_vdw_other 0.286 r_nbd_other 0.243 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.158 r_nbtor_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6594 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing