☰ Navigation Tabs
Crystal structure of the mouse PD-1 and PD-L2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPU 1npu, 1pkq experimental model PDB 1PKQ 1npu, 1pkq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Sitting drop 8.5 291 20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.55 51.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.933 α = 90 b = 84.056 β = 107.88 c = 52.108 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 315 2007-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9792 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 1.7 30 99.2 0.078 9.8 4.6 39403
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 1.7 1.76 97.8 0.573 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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, 1pkq 1.8 24.95 39378 31433 1666 98.62 0.19169 0.1897 0.19 0.22848 0.229 RANDOM 29.223
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] -0.28 0.34 1.34 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.161 r_dihedral_angle_4_deg 20.965 r_dihedral_angle_3_deg 15.806 r_dihedral_angle_1_deg 11.976 r_scangle_it 4.652 r_mcangle_it 4.287 r_scbond_it 3.234 r_mcbond_it 2.987 r_angle_refined_deg 1.347 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.161 r_dihedral_angle_4_deg 20.965 r_dihedral_angle_3_deg 15.806 r_dihedral_angle_1_deg 11.976 r_scangle_it 4.652 r_mcangle_it 4.287 r_scbond_it 3.234 r_mcbond_it 2.987 r_angle_refined_deg 1.347 r_nbtor_refined 0.309 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2406 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction PHASER phasing