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Crystal structure of ULBP6 in complex with a blocking antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 Glycerol 10.0 %v/v MES: 0.10 M pH:6.00 PEG 1K 5.0 %w/v PEG 600 30.0 %w/v
Crystal Properties Matthews coefficient Solvent content 3.34 63.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.551 α = 90 b = 95.803 β = 117.74 c = 97.203 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 EIGER2 S 16M 2022-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.307 86.031 92.3 0.991 7.2 4 19970
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.307 2.658 0.581
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 2.307 86.031 19970 1006 52.373 0.219 0.2159 0.2184 0.2865 0.2836 42.239
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] 0.673 0.182 -0.988 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.953 r_dihedral_angle_3_deg 15.511 r_dihedral_angle_4_deg 13.761 r_dihedral_angle_1_deg 8.385 r_lrange_it 5.15 r_lrange_other 5.149 r_mcangle_it 3.116 r_mcangle_other 3.116 r_scangle_it 2.508 r_scangle_other 2.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.953 r_dihedral_angle_3_deg 15.511 r_dihedral_angle_4_deg 13.761 r_dihedral_angle_1_deg 8.385 r_lrange_it 5.15 r_lrange_other 5.149 r_mcangle_it 3.116 r_mcangle_other 3.116 r_scangle_it 2.508 r_scangle_other 2.508 r_mcbond_it 1.769 r_mcbond_other 1.762 r_angle_refined_deg 1.422 r_scbond_it 1.401 r_scbond_other 1.401 r_angle_other_deg 1.069 r_dihedral_angle_other_1_deg 0.776 r_ext_dist_refined_d 0.443 r_nbd_refined 0.151 r_nbd_other 0.151 r_symmetry_nbd_other 0.15 r_nbtor_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.112 r_symmetry_nbd_refined 0.1 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4617 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing