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Crystal structure of the human tumor necrosis factor receptor 1 extracellular domain at 1.64A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Crystallization cocktail: 0.1 M HEPES, 70% v/v 2-Methyl-2,4-pentanediol (pH 7.5)
Additive cocktail: 0.2% w/v 1,4-diaminobutane, 0.2% w/v 1,8-diaminooctane, 0.2% w/v cadaverine, 0.2% w/v cystamine dihydrochloride, 0.2% w/v Spermidine, 0.02 M HEPES sodium (pH 6.8)
Mixed in 3.5:1:1 (protein/reservoir/additives)
Crystal Properties Matthews coefficient Solvent content 1.85 33.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.221 α = 90 b = 69.221 β = 90 c = 185.186 γ = 90
Symmetry Space Group P 41 21 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 PIXEL DECTRIS EIGER2 XE CdTe 16M KB mirror pair 2024-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7293 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.64 48.95 100 0.112 0.114 0.023 0.999 16.5 25 56257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.7 100 5.972 6.158 1.48 0.117 16.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 THROUGHOUT 1.64 27.72 1.23 56115 2791 99.96 0.2068 0.2052 0.2072 0.2379 0.2144
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 f_dihedral_angle_d 6.562 f_angle_d 1.129 f_chiral_restr 0.056 f_bond_d 0.01 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2073 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 35
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction