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Preclinical Characterization of Pan-NKG2D Ligand-Binding NKG2D Receptor Decoys
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Magnesium Chloride, Tris (pH 8.5), PEG3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.571 α = 90 b = 69.782 β = 90 c = 145.374 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2016-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.85 72.69 83.2 0.092 10.2 2.7 11703
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 87.2 0.502 0.615 0.349 0.794 2.7
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.85 72.69 11066 609 82.98 0.21573 0.21376 0.2155 0.25284 0.2541 RANDOM 55.571
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] -3.64 2.46 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 14.119 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 5.931 r_long_range_B_refined 2.599 r_long_range_B_other 2.599 r_scangle_other 1.535 r_mcangle_it 1.222 r_mcangle_other 1.222 r_angle_refined_deg 1.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.614 r_dihedral_angle_4_deg 14.119 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 5.931 r_long_range_B_refined 2.599 r_long_range_B_other 2.599 r_scangle_other 1.535 r_mcangle_it 1.222 r_mcangle_other 1.222 r_angle_refined_deg 1.141 r_scbond_it 0.904 r_scbond_other 0.904 r_angle_other_deg 0.843 r_mcbond_it 0.664 r_mcbond_other 0.664 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3325 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing