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Crystal structure of the TIR domain of human TLR1 (crystallised without ZN2+ ions)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 277 170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton)
Growth at +4 for 3-4 months.
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.26 α = 90 b = 101.26 β = 90 c = 68.85 γ = 120
Symmetry Space Group P 62 2 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 PILATUS 6M 2020-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.47 50.63 99.92 0.02972 0.999 21.19 37.5 7879 53.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.558 0.2996 0.836
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1FYV 2.47 50.63 7876 398 99.95 0.2317 0.2292 0.2368 0.2788 0.2838 55.61
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 10.7587 f_angle_d 0.3907 f_chiral_restr 0.0396 f_plane_restr 0.0034 f_bond_d 0.0013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1296 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling PHASER phasing