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Complex structure of PD1 and 609A-Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M Ammonium formate, pH 6.6, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.29 α = 90 b = 68.41 β = 99.44 c = 77.31 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2020-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.64 48.91 99.7 0.049 0.067 0.045 0.996 12.5 3.3 70749
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 1.64 1.67 99.9 0.457 0.618 0.413 0.842 2.2 3.4
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 5WT9 1.64 48.91 67222 3529 99.69 0.1617 0.1596 0.1734 0.2019 0.2123 RANDOM 20.227
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] 0.74 -0.43 -0.07 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.292 r_dihedral_angle_1_deg 20.713 r_dihedral_angle_4_deg 17.831 r_dihedral_angle_3_deg 12.235 r_angle_refined_deg 1.784 r_angle_other_deg 1.472 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.292 r_dihedral_angle_1_deg 20.713 r_dihedral_angle_4_deg 17.831 r_dihedral_angle_3_deg 12.235 r_angle_refined_deg 1.784 r_angle_other_deg 1.472 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4227 Nucleic Acid Atoms Solvent Atoms 789 Heterogen Atoms 94
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction