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Structure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TZE, 1MUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293.15 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 4.21 70.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.994 α = 90 b = 184.994 β = 90 c = 122.672 γ = 120
Symmetry Space Group P 65 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 EIGER2 XE 9M 2024-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97856 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 4.66 92.5 99.8 0.187 0.198 0.992 10.91 10.5 7006 232.6
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 4.66 4.94 99.4 2.57 0.387 1.13 11.2
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 SAD FREE R-VALUE 4.66 92.5 1.34 6998 351 99.84 0.2709 0.268 0.2741 0.3257 0.3347
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 11.557 f_angle_d 0.569 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4643 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing