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Macaque CD1d with lipid antigen bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 10% w/v PEG 8000, 20% v/v ethylene glycol 0.03 M, 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.97 58.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.0613 α = 90 b = 87.0613 β = 90 c = 232.805 γ = 120
Symmetry Space Group P 32 2 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 2022-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.83 54.08 98.22 0.056 0.013 1 32.7 17.1 89434 24.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 84.73 0.486 0.179 0.914 2.1 6.7
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.83 54.076 89349 2075 98.12 0.171 0.1707 0.2171 0.2161 33.15
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] 2.81595458 2.81595458 -5.63190917
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.2774 s_dihedral_angle_3_deg 12.2411 s_dihedral_angle_1_deg 7.2225 s_dihedral_angle_2_deg 3.0335 s_angle_nonh_deg 2.0335 s_nbtor 0.2246 s_nbd 0.2141 s_symmetry_hbond_nbd 0.1974 s_symmetry_nbd 0.1928 s_hbond_nbd 0.1671
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.2774 s_dihedral_angle_3_deg 12.2411 s_dihedral_angle_1_deg 7.2225 s_dihedral_angle_2_deg 3.0335 s_angle_nonh_deg 2.0335 s_nbtor 0.2246 s_nbd 0.2141 s_symmetry_hbond_nbd 0.1974 s_symmetry_nbd 0.1928 s_hbond_nbd 0.1671 s_chiral_restr 0.0977 s_planes 0.0153 s_bond_nonh_d 0.0137
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6056 Nucleic Acid Atoms Solvent Atoms 1070 Heterogen Atoms 151
Software Software Software Name Purpose DIALS data reduction xia2 data scaling gemmi data extraction MOLREP phasing Coot model building Servalcat refinement