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Crystal strucutre of PD-L1 and the computationally designed DBL1_03 protein binder
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 291 0.02 M nickel (II) chloride hexahydrate, 0.02 M magnesium chloride hexahydrate, 0.02 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate, pH4.5, 24% w/v polyethylene glycol monomethylether 2000
Crystal Properties Matthews coefficient Solvent content 3.35 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.93 α = 90 b = 97.93 β = 90 c = 106.11 γ = 90
Symmetry Space Group P 42 21 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 CCD ADSC QUANTUM 315r 2019-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97889 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.85 48.97 99.9 0.141 0.998 20.7 25.4 12591 1.36 124.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.95 100 3.126 0.554 1.1 26.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.85 48.97 1.35 12582 630 99.93 0.3006 0.2996 0.3182 0.3037 124.12
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 6.8549 f_angle_d 1.254 f_chiral_restr 0.0617 f_bond_d 0.0099 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2619 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing