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Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WSL experimental model PDB 3RRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris pH 8.5, 25% w/v PEG 3,350, 20% w/v MPD
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.839 α = 90 b = 70.241 β = 90 c = 163.684 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2024-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 1.85 81.84 100 0.106 0.11 0.03 0.999 13.9 13.1 61790 29.7
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 1.85 1.89 100 1.523 1.589 0.448 0.716 1.8 12.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 81.84 61683 3096 99.955 0.18 0.1778 0.2159 0.2079 32.183
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] 0.106 -0.21 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.137 r_dihedral_angle_6_deg 13.909 r_dihedral_angle_3_deg 12.714 r_lrange_it 8.093 r_lrange_other 8.093 r_dihedral_angle_1_deg 7.311 r_scangle_it 6.769 r_scangle_other 6.768 r_scbond_it 4.697 r_scbond_other 4.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.137 r_dihedral_angle_6_deg 13.909 r_dihedral_angle_3_deg 12.714 r_lrange_it 8.093 r_lrange_other 8.093 r_dihedral_angle_1_deg 7.311 r_scangle_it 6.769 r_scangle_other 6.768 r_scbond_it 4.697 r_scbond_other 4.696 r_mcangle_other 3.939 r_mcangle_it 3.938 r_mcbond_it 2.988 r_mcbond_other 2.987 r_angle_other_deg 1.959 r_angle_refined_deg 1.777 r_nbd_other 0.344 r_symmetry_nbd_other 0.223 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_other 0.133 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.111 r_gen_planes_other 0.015 r_gen_planes_refined 0.014 r_bond_refined_d 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4070 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing