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Crystal Structure of DcR3-TL1A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QE3 PDB ENTRY 2QE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 290 0.1M MES pH6.5, 8% PEG 10K, 3% dextran sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.89 α = 90 b = 74.89 β = 90 c = 143.125 γ = 120
Symmetry Space Group P 3 2 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 ADSC QUANTUM 315 2008-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E APS 24-ID-E
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 2.45 50 99.9 0.131 15.3 7.7 17791 47.85
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) 2.45 2.49 100 0.99 3.17 7.6
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 PDB ENTRY 2QE3 2.45 36.23 17779 566 99.9 0.224 0.223 0.2217 0.262 0.2552 RANDOM 79.96
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] -3.27 -1.63 -3.27 4.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.375 r_dihedral_angle_4_deg 16.151 r_dihedral_angle_3_deg 15.111 r_dihedral_angle_1_deg 6.262 r_scangle_it 5.97 r_scbond_it 4.026 r_mcangle_it 3.909 r_mcbond_it 2.194 r_angle_refined_deg 0.54 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.375 r_dihedral_angle_4_deg 16.151 r_dihedral_angle_3_deg 15.111 r_dihedral_angle_1_deg 6.262 r_scangle_it 5.97 r_scbond_it 4.026 r_mcangle_it 3.909 r_mcbond_it 2.194 r_angle_refined_deg 0.54 r_nbtor_refined 0.319 r_xyhbond_nbd_refined 0.201 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.136 r_chiral_restr 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction