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Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.1M Sodium citrate pH 5, 20% PEG 8000, Vapor diffusion, Sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.77 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.778 α = 90 b = 62.843 β = 90 c = 160.863 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 CCD ADSC QUANTUM 315 2007-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.071 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.28 50 99.9 0.093 7.6 6.1 26816 26816
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 2.28 2.38 100 0.729 6.1 2628
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 1NPU 2.28 31.42 26756 1339 99.11 0.221 0.2184 0.2128 0.2704 0.2622 RANDOM 43.3543
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] -0.33 -1.72 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.774 r_dihedral_angle_4_deg 21.329 r_dihedral_angle_3_deg 16.418 r_dihedral_angle_1_deg 6.423 r_scangle_it 2.969 r_scbond_it 1.84 r_angle_refined_deg 1.421 r_mcangle_it 1.295 r_mcbond_it 0.69 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.774 r_dihedral_angle_4_deg 21.329 r_dihedral_angle_3_deg 16.418 r_dihedral_angle_1_deg 6.423 r_scangle_it 2.969 r_scbond_it 1.84 r_angle_refined_deg 1.421 r_mcangle_it 1.295 r_mcbond_it 0.69 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3429 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing