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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 3.19 61.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.785 α = 90 b = 136.785 β = 90 c = 69.797 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 2021-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.8 48.85 100 0.229 0.238 0.064 0.983 7 13.8 443095
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 2.8 2.95 0.862 0.983 2.3
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 2.80001551676 48.3608005323 1.33784080954 32013 1642 99.8284894599 0.209745531039 0.207530559523 0.2118 0.24941654438 0.2518 73.4051560046
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 15.6918570457 f_angle_d 0.816954377624 f_chiral_restr 0.0495436338867 f_bond_d 0.00590741541861 f_plane_restr 0.00539184030008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6296 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 124
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing