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Crystal structure of a complex between glycosylated NKp30 and its deglycosylated tumour ligand B7-H6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.7 294 0.1 M sodium citrate pH 6.7, 11.7 % PEG 6000, 10 mg/ml mixture of both proteins, micro-seeded with crushed needle-shaped crystals
Crystal Properties Matthews coefficient Solvent content 3.54 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.044 α = 90 b = 86.462 β = 97.58 c = 111.299 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F 2016-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 3.1 48.95 95 0.104 0.134 0.081 0.995 5.7 3.7 27102 105.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.29 87 0.971 0.804 0.645 0.8 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3PV6 3.1 48.95 25738 1348 94.72 0.2748 0.2723 0.2715 0.3221 0.3261 RANDOM 155.577
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] 19.96 5.37 -5.81 -15.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.713 r_dihedral_angle_3_deg 21.118 r_dihedral_angle_4_deg 19.778 r_dihedral_angle_1_deg 6.952 r_angle_refined_deg 1.59 r_chiral_restr 0.12 r_gen_planes_refined 0.009 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6837 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing PHASER phasing