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Crystal Structure of the 4-1BB/4-1BBL Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M Potassium citrate tribasic monohydrate
20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.571 α = 90 b = 161.571 β = 90 c = 161.571 γ = 90
Symmetry Space Group I 21 3
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 R CdTe 300K 2017-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.4 38 100 0.165 0.173 0.053 0.994 12.4 20.6 27518 46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.6 1.449 1.523 0.467 0.799 2.5 10.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2X29 2.4 38 26418 1086 99.95 0.22799 0.22651 0.26479 0.2747 RANDOM 62.182
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.542 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_3_deg 13.007 r_long_range_B_refined 7.006 r_long_range_B_other 6.998 r_dihedral_angle_1_deg 6.511 r_scangle_other 4.743 r_mcangle_it 4.396 r_mcangle_other 4.396 r_scbond_it 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.542 r_dihedral_angle_4_deg 15.241 r_dihedral_angle_3_deg 13.007 r_long_range_B_refined 7.006 r_long_range_B_other 6.998 r_dihedral_angle_1_deg 6.511 r_scangle_other 4.743 r_mcangle_it 4.396 r_mcangle_other 4.396 r_scbond_it 2.927 r_scbond_other 2.927 r_mcbond_it 2.751 r_mcbond_other 2.751 r_angle_refined_deg 1.122 r_angle_other_deg 0.827 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4150 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing