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Crystal Structure of Human TL1A Extracellular Domain C95S Mutant
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 VAPOR DIFFUSION, SITTING DROP 8.5 298 10 MM CACL2, 100 MM TRIS, PH 8.50, 20% METHONAL, VAPOR DIFFUSION, SITTING DROP, TEMPERATUR 290K, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.226 α = 90 b = 118.226 β = 90 c = 118.226 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 2007-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97910 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 2.3 50 99.9 0.085 0.062 40.5 22 13160
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) 2.3 2.38 100 0.878 0.783 3.33 15.9
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 2.3 25.8 12705 400 99.86 0.21332 0.21183 0.2082 0.26507 0.2606 RANDOM 52.622
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 36.718 r_dihedral_angle_4_deg 19.813 r_dihedral_angle_3_deg 14.989 r_scangle_it 9.163 r_mcangle_it 8.658 r_scbond_it 8.231 r_dihedral_angle_1_deg 7.963 r_mcbond_it 5.839 r_angle_refined_deg 1.682 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.718 r_dihedral_angle_4_deg 19.813 r_dihedral_angle_3_deg 14.989 r_scangle_it 9.163 r_mcangle_it 8.658 r_scbond_it 8.231 r_dihedral_angle_1_deg 7.963 r_mcbond_it 5.839 r_angle_refined_deg 1.682 r_nbtor_refined 0.324 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 1140 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling