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Crystal structure of 4-1BB in complex with a VHH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MGP 6MGP, 4XTA experimental model PDB 4XTA 6MGP, 4XTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291 1.5 M lithium sulfate, 100 mM Tris (pH 8.5), 10 mM nickel sulfate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.851 α = 90 b = 106.851 β = 90 c = 146.41 γ = 90
Symmetry Space Group P 41 21 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 PIXEL DECTRIS PILATUS3 S 6M 2020-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.14 47.79 99.9 0.162 0.047 0.998 16.1 12.9 15429
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 3.14 3.36 99.8 1.241 0.359 0.894 12.8
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 6MGP, 4XTA 3.14 47.79 14654 726 99.88 0.2136 0.2113 0.219 0.2581 0.2566 RANDOM 90.054
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] 4.12 4.12 -8.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 21.843 r_dihedral_angle_3_deg 19.981 r_dihedral_angle_1_deg 9.261 r_angle_refined_deg 2.142 r_angle_other_deg 1.555 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 21.843 r_dihedral_angle_3_deg 19.981 r_dihedral_angle_1_deg 9.261 r_angle_refined_deg 2.142 r_angle_other_deg 1.555 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1994 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling PHASER phasing