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KIR3DL1*001 in complex with HLA-A*24:02 presenting the TW9 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 294 16% PEG-3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.437 α = 93.444 b = 62.119 β = 100.673 c = 67 γ = 109.966
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 2022-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 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 48.09 97.4 0.04 0.998 14.1 3.3 50901 41.66
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 2.05 0.342 0.926 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 35.88 2.01 50879 2511 97.35 0.2115 0.2105 0.2101 0.2312 0.232 60.89
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 14.0403 f_angle_d 0.8823 f_chiral_restr 0.0541 f_plane_restr 0.0082 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5148 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing