☰ Navigation Tabs
Crystal structures of the murine class I major histocompatibility complex H-2Dbm13 in complex with adenovirus-derived peptide Ad10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 1.8M ammonium sulphate, 0.1M Tris
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.41 α = 83.98 b = 70.27 β = 86.9 c = 87.05 γ = 81.75
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 210r 2008-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 20 97.1 0.121 7 3.1 42580
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.57 0.57
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 1N5A 2.4 19.94 39771 2133 96.98 0.2026 0.20012 0.2061 0.24869 0.2549 RANDOM 54.597
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] 0.17 0.06 -0.04 -0.22 0.28 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.742 r_dihedral_angle_4_deg 19.278 r_dihedral_angle_3_deg 19.054 r_long_range_B_refined 8.68 r_long_range_B_other 8.68 r_dihedral_angle_1_deg 6.398 r_scangle_other 5.68 r_mcangle_it 5.022 r_mcangle_other 5.021 r_scbond_it 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.742 r_dihedral_angle_4_deg 19.278 r_dihedral_angle_3_deg 19.054 r_long_range_B_refined 8.68 r_long_range_B_other 8.68 r_dihedral_angle_1_deg 6.398 r_scangle_other 5.68 r_mcangle_it 5.022 r_mcangle_other 5.021 r_scbond_it 3.498 r_scbond_other 3.497 r_mcbond_it 3.124 r_mcbond_other 3.124 r_angle_refined_deg 1.443 r_angle_other_deg 1.11 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6266 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing