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Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D0G TRAIL FROM 1D0G AND DR4 FROM 1DOG DR5 experimental model PDB 1DOG TRAIL FROM 1D0G AND DR4 FROM 1DOG DR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 100 mM MMT (1:2:2 ratio of DL-malic acid, MES, Tris base), pH 5.0, 22.2%(W/V) PEG 2000MME
Crystal Properties Matthews coefficient Solvent content 2.12 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.6 α = 90 b = 87.6 β = 90 c = 107.7 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2009-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 3 50 99.8 0.092 20.8 7.3 16742 71.79
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 3 3.11 100 0.365 6.4 7.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT TRAIL FROM 1D0G AND DR4 FROM 1DOG DR5 3 27.6 16541 1049 99.89 0.1792 0.1767 0.1833 0.2163 0.2287 RANDOM 42.22
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] 4.728 -8.4057 3.6777
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.72 t_omega_torsion 3.36 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.72 t_omega_torsion 3.36 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5601 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 2
Software Software Software Name Purpose BUSTER-TNT refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing