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Crystal structure of 4-1BBL/4-1BB complex in C2 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X29 2X29, 5WI8 experimental model PDB 5WI8 2X29, 5WI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M Na acetate pH 4.6
10% W/V PEG 4000
0.2M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.49 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.28 α = 90 b = 66.504 β = 103.09 c = 129.356 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 2018-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 38 97.7 0.143 0.156 0.993 7.8 5.744 25892 61.482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 95.4 0.921 1.022 0.817 1.95 5.016
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 2X29, 5WI8 2.7 38 24498 1320 97.54 0.2503 0.2487 0.2553 0.2796 0.2896 RANDOM 61.638
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] -4.38 1.91 -3.1 5.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_4_deg 18.776 r_dihedral_angle_3_deg 16.249 r_dihedral_angle_1_deg 7.094 r_angle_refined_deg 1.346 r_angle_other_deg 0.942 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.951 r_dihedral_angle_4_deg 18.776 r_dihedral_angle_3_deg 16.249 r_dihedral_angle_1_deg 7.094 r_angle_refined_deg 1.346 r_angle_other_deg 0.942 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6022 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing