☰ Navigation Tabs
Crystal structure of ALPN-202 (engineered CD80 vIgD) in complex with PD-L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DR9 1DR9, 5JDR experimental model PDB 5JDR 1DR9, 5JDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.03 M sodium nitrate, 0.03 M sodium
phosphate dibasic, 0.03 M ammonium sulfate, 0.1 M sodium HEPES/MOPS (acid), pH 7.5, 20% v/v glycerol, 10% w/v
PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.85 68.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.928 α = 90 b = 122.152 β = 90 c = 152.675 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 2019-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.15 95.38 99.3 0.996 0.9 5.4 19918
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.37 1.722
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 1DR9, 5JDR 3.15 76.34 19859 991 99 0.2496 0.2474 0.2448 0.2909 0.2983 RANDOM 110.9
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] 16.2071 -31.8755 15.6684
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.44 t_omega_torsion 2.82 t_angle_deg 1.06 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.44 t_omega_torsion 2.82 t_angle_deg 1.06 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5021 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 242
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing