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Complex assembly, crystallization and preliminary X-ray crystallographic studies of duck MHC class I molecule
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 2% v/v Tacsimate TM pH 7.0
0.1 M HEPES pH 7.5
20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.468 α = 90 b = 82.468 β = 90 c = 112.507 γ = 120
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 2019-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97931 SSRF BL18U1
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 1.26 19.85 86.26 0.086 0.086 12.6 14.6 101015
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 1.26 1.3 0.086 0.086
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.5 19.81 69095 3477 99.831 0.167 0.1662 0.1662 0.1878 0.1876 22.042
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 r_dihedral_angle_2_deg 34.316 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 13.826 r_dihedral_angle_1_deg 6.6 r_lrange_it 6.408 r_lrange_other 6.144 r_scangle_it 5.033 r_scangle_other 5.032 r_scbond_it 3.321 r_scbond_other 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 13.826 r_dihedral_angle_1_deg 6.6 r_lrange_it 6.408 r_lrange_other 6.144 r_scangle_it 5.033 r_scangle_other 5.032 r_scbond_it 3.321 r_scbond_other 3.32 r_mcangle_other 2.541 r_mcangle_it 2.54 r_mcbond_it 1.745 r_angle_refined_deg 1.739 r_mcbond_other 1.739 r_angle_other_deg 1.479 r_symmetry_xyhbond_nbd_refined 0.341 r_xyhbond_nbd_other 0.232 r_xyhbond_nbd_refined 0.215 r_nbd_refined 0.207 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.175 r_nbd_other 0.167 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3095 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing