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Crystal structure of human tl1a extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TNF PDB ENTRY 2TNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 10 MM CACL2, 100 MM TRIS, PH 8.50, 20% METHONAL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.48 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.404 α = 90 b = 120.404 β = 90 c = 120.404 γ = 90
Symmetry Space Group P 41 3 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 315 MIRRORS 2007-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.5 50 99.9 0.17 0.124 3.5 21.1 10856 54.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.56 0.96 1.7 10.6
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 2TNF 2.5 19.8 10462 323 99.98 0.21085 0.20929 0.2081 0.26336 0.2661 RANDOM 51.137
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 r_dihedral_angle_2_deg 37.538 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_4_deg 17.171 r_scangle_it 14.697 r_scbond_it 11.975 r_mcangle_it 11.473 r_dihedral_angle_1_deg 11.062 r_mcbond_it 9.372 r_angle_refined_deg 2.355 r_nbtor_refined 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.538 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_4_deg 17.171 r_scangle_it 14.697 r_scbond_it 11.975 r_mcangle_it 11.473 r_dihedral_angle_1_deg 11.062 r_mcbond_it 9.372 r_angle_refined_deg 2.355 r_nbtor_refined 0.355 r_symmetry_hbond_refined 0.289 r_xyhbond_nbd_refined 0.255 r_nbd_refined 0.244 r_symmetry_vdw_refined 0.178 r_chiral_restr 0.142 r_bond_refined_d 0.027 r_gen_planes_refined 0.009 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 1121 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 1
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling