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Crystal structures of the murine class I major histocompatibility complex H-2Db 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 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.14 α = 84.2 b = 69.24 β = 86.69 c = 87.16 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 2009-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.00 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 2.34 20 90 0.137 8.5 3.5 42622
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 2.34 2.5 0.64
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 19.98 38969 2000 96.65 0.1999 0.19815 0.2022 0.23333 0.2364 RANDOM 48.314
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] -0.09 0.11 0.04 0.27 0.32 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_4_deg 21.845 r_dihedral_angle_3_deg 18.428 r_long_range_B_other 9.936 r_long_range_B_refined 9.933 r_dihedral_angle_1_deg 7.096 r_scangle_other 7.035 r_mcangle_it 6.163 r_mcangle_other 6.163 r_scbond_it 4.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_4_deg 21.845 r_dihedral_angle_3_deg 18.428 r_long_range_B_other 9.936 r_long_range_B_refined 9.933 r_dihedral_angle_1_deg 7.096 r_scangle_other 7.035 r_mcangle_it 6.163 r_mcangle_other 6.163 r_scbond_it 4.408 r_scbond_other 4.405 r_mcbond_it 3.906 r_mcbond_other 3.905 r_angle_refined_deg 1.76 r_angle_other_deg 1.165 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 6264 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing