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Complex structure of GY-5 Fab and PD-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RRQ 3RRQ, 3EYQ experimental model PDB 3EYQ 3RRQ, 3EYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 277 0.1 M citrate (pH 5.0), 20% w/v polyethylene glycol 6000, 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.595 α = 90 b = 64.347 β = 98.04 c = 151.481 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 100 CCD ADSC QUANTUM 315r 2016-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.6 50 92.2 3.17 6.2 33831
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3RRQ, 3EYQ 2.6 41.624 1.34 33831 1698 92.24 0.2148 0.2116 0.2119 0.2767 0.275
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 f_dihedral_angle_d 19.98 f_angle_d 1.248 f_chiral_restr 0.07 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8342 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing