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Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and TCR Beta-Chain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZT4 experimental model PDB 4GG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350, sodium citrate, citrate-bis-Tris pH7
Crystal Properties Matthews coefficient Solvent content 3.27 62.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.788 α = 90 b = 133.788 β = 90 c = 68.574 γ = 90
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 EIGER X 16M 2021-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 47.30121 100 0.092 0.997 11.5 7.1 298286 49.1948800742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.428 0.899 3.7 7.1
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 FREE R-VALUE 2.50000221525 47.3012010207 1.34973869404 42254 2145 99.9763392012 0.186670583574 0.184181740466 0.1887 0.234109300748 0.2396 51.2244445572
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 15.5832256546 f_angle_d 0.988735177298 f_chiral_restr 0.0557915855357 f_bond_d 0.00815511180277 f_plane_restr 0.00549452545341
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6305 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing