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TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HZH PDB ENTRY 1HZH for Fab, PDB ENTRY 1D4V for TRAIL-R2 experimental model PDB 1D4V PDB ENTRY 1HZH for Fab, PDB ENTRY 1D4V for TRAIL-R2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 7.5% PEG 3350, 75mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.974 α = 90 b = 151.563 β = 90 c = 65.044 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 315r 2005-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 47.7 94.9 0.08 12.1 4.9 41507 39887
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 2.1 2.18 84.2 0.294 1.9 2.7 3472
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 PDB ENTRY 1HZH for Fab, PDB ENTRY 1D4V for TRAIL-R2 2.1 47.67 39887 39887 1994 94.82 0.18801 0.18801 0.18612 0.1864 0.2236 0.224 RANDOM 32.808
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] -0.15 0.51 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.196 r_dihedral_angle_4_deg 20.588 r_dihedral_angle_3_deg 16.665 r_dihedral_angle_1_deg 6.551 r_long_range_B_refined 5.63 r_mcangle_it 1.764 r_angle_refined_deg 1.357 r_scbond_it 1.307 r_mcbond_it 1.004 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.196 r_dihedral_angle_4_deg 20.588 r_dihedral_angle_3_deg 16.665 r_dihedral_angle_1_deg 6.551 r_long_range_B_refined 5.63 r_mcangle_it 1.764 r_angle_refined_deg 1.357 r_scbond_it 1.307 r_mcbond_it 1.004 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3878 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 45
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling