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Racemic structure of TNFR1 cysteine-rich domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 250 nL of DL-TNFR-1 CRD2 (25 mg/mL) and 250 nL of precipitant (1.5 M Sodium chloride, 10% v/v ethanol, pH 8.5) were mixed in the sitting drop. The single, block shaped crystal was dipped into 2.0 M lithium sulfate and flash frozen in liquid nitrogen during harvesting.
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.42 α = 90 b = 50.49 β = 92.94 c = 46.21 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 XE 16M 2021-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.6767 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.4 34.06 100 0.999 11.3 6.01 18553
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 0.785 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 34.06 17590 943 99.98 0.20274 0.20022 0.2015 0.25144 0.2514 14.739
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] -1.24 0.11 -0.48 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.675 r_dihedral_angle_3_deg 18.454 r_dihedral_angle_1_deg 7.42 r_rigid_bond_restr 4.395 r_long_range_B_refined 3.705 r_long_range_B_other 3.231 r_scangle_other 1.693 r_angle_refined_deg 1.662 r_scbond_it 1.441 r_mcangle_it 1.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.675 r_dihedral_angle_3_deg 18.454 r_dihedral_angle_1_deg 7.42 r_rigid_bond_restr 4.395 r_long_range_B_refined 3.705 r_long_range_B_other 3.231 r_scangle_other 1.693 r_angle_refined_deg 1.662 r_scbond_it 1.441 r_mcangle_it 1.399 r_mcangle_other 1.398 r_scbond_other 1.233 r_mcbond_it 1.041 r_mcbond_other 1.026 r_angle_other_deg 0.654 r_chiral_restr 0.102 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 738 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing Coot model building