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Human 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 8.2 293.15 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.6218 α = 90 b = 156.3734 β = 90 c = 51.9093 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2021-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9253 ESRF ID30B
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 1.76 49.27 96.62 0.094 0.049 0.968 14.8 3.3 92489 24.95
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 1.76 1.79 71.07 0.937 0.487 0.532 1.1 3.1
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 1.76 49.266 92323 2016 96.44 0.2132 0.2121 0.2542 0.254 35.42
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] 4.77060556 -1.06836745 -3.70223811
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.1817 s_dihedral_angle_3_deg 11.7448 s_dihedral_angle_1_deg 7.3264 s_dihedral_angle_2_deg 4.9407 s_angle_nonh_deg 2.0822 s_nbtor 0.2238 s_nbd 0.2216 s_symmetry_nbd 0.2151 s_symmetry_hbond_nbd 0.1926 s_hbond_nbd 0.182
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.1817 s_dihedral_angle_3_deg 11.7448 s_dihedral_angle_1_deg 7.3264 s_dihedral_angle_2_deg 4.9407 s_angle_nonh_deg 2.0822 s_nbtor 0.2238 s_nbd 0.2216 s_symmetry_nbd 0.2151 s_symmetry_hbond_nbd 0.1926 s_hbond_nbd 0.182 s_chiral_restr 0.0938 s_planes 0.0152 s_bond_nonh_d 0.0132
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6028 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 152
Software Software Software Name Purpose xia2 data scaling DIALS data reduction gemmi data extraction MOLREP phasing Coot model building Servalcat refinement