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Crystal structure of Fab-Lirilumab bound to KIR2DL3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B6U Model for KIR2DL3 experimental model PDB 6XOC Fab was extracted from this model, and phenix's sculpt program was used as a preliminary model the lirilumab similar Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 200 mM Potassium Sodium Tartrate and 20%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.68 26.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.379 α = 90 b = 84.27 β = 115.86 c = 62.268 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2021-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.75 50 98.5 0.138 0.146 0.058 14 6.5 13977 60.85
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 2.75 2.8 98.1 0.92 0.759 5.9
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 2.75 46.66 1.36 13574 570 95.31 0.2126 0.2109 0.2102 0.254 0.2533 68.5
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 16.2975 f_angle_d 1.1339 f_chiral_restr 0.0742 f_bond_d 0.0083 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing