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Human NK cell receptor NKp80, extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9NZS2-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.8M Succinic Acid
0.1M Tris
Crystal Properties Matthews coefficient Solvent content 2.86 56.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.544 α = 90 b = 183.544 β = 90 c = 123.668 γ = 120
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 2023-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.9 158.95 93.9 0.641 0.714 0.304 0.962 3.1 9.2 49380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 12.872 5.579 0.026 9.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 97.607 49349 2339 93.893 0.223 0.221 0.2209 0.2572 0.2571 96.3
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] 2.099 1.05 2.099 -6.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.197 r_lrange_it 21.515 r_scangle_it 18.245 r_dihedral_angle_6_deg 16.803 r_mcangle_it 13.585 r_scbond_it 12.597 r_dihedral_angle_1_deg 9.479 r_mcbond_it 8.786 r_dihedral_angle_2_deg 8.44 r_angle_refined_deg 2.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.197 r_lrange_it 21.515 r_scangle_it 18.245 r_dihedral_angle_6_deg 16.803 r_mcangle_it 13.585 r_scbond_it 12.597 r_dihedral_angle_1_deg 9.479 r_mcbond_it 8.786 r_dihedral_angle_2_deg 8.44 r_angle_refined_deg 2.413 r_nbtor_refined 0.304 r_symmetry_nbd_refined 0.291 r_symmetry_xyhbond_nbd_refined 0.28 r_nbd_refined 0.214 r_chiral_restr 0.188 r_xyhbond_nbd_refined 0.118 r_ncsr_local_group_2 0.106 r_ncsr_local_group_21 0.102 r_ncsr_local_group_8 0.1 r_ncsr_local_group_10 0.099 r_ncsr_local_group_23 0.098 r_ncsr_local_group_19 0.097 r_ncsr_local_group_27 0.097 r_ncsr_local_group_4 0.096 r_ncsr_local_group_12 0.095 r_ncsr_local_group_16 0.095 r_ncsr_local_group_41 0.095 r_ncsr_local_group_3 0.094 r_ncsr_local_group_18 0.094 r_ncsr_local_group_32 0.094 r_ncsr_local_group_36 0.093 r_ncsr_local_group_42 0.093 r_ncsr_local_group_11 0.092 r_ncsr_local_group_7 0.091 r_ncsr_local_group_5 0.089 r_ncsr_local_group_22 0.089 r_ncsr_local_group_31 0.089 r_ncsr_local_group_40 0.089 r_ncsr_local_group_20 0.088 r_ncsr_local_group_24 0.088 r_ncsr_local_group_6 0.087 r_ncsr_local_group_13 0.087 r_ncsr_local_group_9 0.086 r_ncsr_local_group_34 0.086 r_ncsr_local_group_14 0.084 r_ncsr_local_group_15 0.083 r_ncsr_local_group_25 0.083 r_ncsr_local_group_1 0.082 r_ncsr_local_group_17 0.082 r_ncsr_local_group_35 0.082 r_ncsr_local_group_26 0.081 r_ncsr_local_group_43 0.081 r_ncsr_local_group_38 0.08 r_ncsr_local_group_45 0.079 r_ncsr_local_group_29 0.077 r_ncsr_local_group_30 0.077 r_ncsr_local_group_33 0.075 r_ncsr_local_group_39 0.072 r_ncsr_local_group_44 0.07 r_ncsr_local_group_28 0.069 r_ncsr_local_group_37 0.064 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10219 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing