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Crystal structure of CD137 in complex with the cyclic peptide BCY10916
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293.15 1.5 M lithium sulfate monohydrate, 0.1M sodium acetate trihydrate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.92 68.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.47 α = 90 b = 122.47 β = 90 c = 122.47 γ = 90
Symmetry Space Group P 42 3 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 EIGER2 XE 16M 2019-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.01 40.857 100 0.042 0.043 1 45.7 39.1 21496
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 2.01 2.05 2.216 2.244 0.756
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6MI2 2.011 40.857 21467 1070 99.851 0.285 0.2831 0.2832 0.314 0.3144 63.013
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_other_3_deg 39.94 r_dihedral_angle_2_deg 28.803 r_dihedral_angle_3_deg 17.881 r_lrange_other 12.366 r_lrange_it 12.36 r_dihedral_angle_4_deg 11.678 r_scangle_it 9.773 r_scangle_other 9.767 r_mcangle_it 8.164 r_mcangle_other 8.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 39.94 r_dihedral_angle_2_deg 28.803 r_dihedral_angle_3_deg 17.881 r_lrange_other 12.366 r_lrange_it 12.36 r_dihedral_angle_4_deg 11.678 r_scangle_it 9.773 r_scangle_other 9.767 r_mcangle_it 8.164 r_mcangle_other 8.158 r_dihedral_angle_1_deg 8.054 r_scbond_it 7.12 r_scbond_other 7.113 r_mcbond_it 6.076 r_mcbond_other 6.07 r_angle_other_deg 2.464 r_angle_refined_deg 1.798 r_nbd_other 0.278 r_symmetry_nbd_other 0.234 r_nbd_refined 0.231 r_symmetry_nbd_refined 0.204 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.043 r_bond_other_d 0.037 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1072 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing