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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 Peg 3350, DL-Malic acid (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 4.18 70.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.823 α = 90 b = 127.823 β = 90 c = 157.017 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315r 2016-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97648 ALS 5.0.1
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 2.75 110.7 99.9 0.077 19.5 12.3 20359
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 2.75 2.8 100 0.752 0.786 0.221 0.937 12.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.75 110.7 19230 1054 99.66 0.23257 0.23047 0.26999 0.2783 RANDOM 76.392
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] -1.24 -0.62 -1.24 4.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.014 r_dihedral_angle_4_deg 17.382 r_dihedral_angle_3_deg 12.224 r_dihedral_angle_1_deg 5.611 r_long_range_B_refined 4.478 r_long_range_B_other 4.476 r_scangle_other 2.867 r_mcangle_it 2.263 r_mcangle_other 2.263 r_scbond_it 1.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.014 r_dihedral_angle_4_deg 17.382 r_dihedral_angle_3_deg 12.224 r_dihedral_angle_1_deg 5.611 r_long_range_B_refined 4.478 r_long_range_B_other 4.476 r_scangle_other 2.867 r_mcangle_it 2.263 r_mcangle_other 2.263 r_scbond_it 1.665 r_scbond_other 1.661 r_mcbond_it 1.28 r_mcbond_other 1.28 r_angle_refined_deg 1.241 r_angle_other_deg 0.845 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 2637 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing