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Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPU 1NPU,3BOV experimental model PDB 3BOV 1NPU,3BOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1M HEPES pH 7, 0.1M Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.75 29.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.057 α = 90 b = 60.246 β = 90 c = 80.087 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 2008-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.74 50 95.1 0.62 0.63 26.23 5.9 17532 17532
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.81 69.6 0.155 0.16 4.42 2.4
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 1NPU,3BOV 1.74 48.17 17485 909 94.39 0.1974 0.1947 0.1946 0.2469 0.2455 RANDOM 25.5806
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] -1.55 3.2 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_4_deg 19.014 r_dihedral_angle_3_deg 14.876 r_dihedral_angle_1_deg 6.661 r_scangle_it 3.878 r_scbond_it 2.317 r_mcangle_it 1.812 r_angle_refined_deg 1.412 r_mcbond_it 0.971 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_4_deg 19.014 r_dihedral_angle_3_deg 14.876 r_dihedral_angle_1_deg 6.661 r_scangle_it 3.878 r_scbond_it 2.317 r_mcangle_it 1.812 r_angle_refined_deg 1.412 r_mcbond_it 0.971 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1700 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing