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Crystal Structure Of The Murine Class I Major Histocompatibility Complex Of H-2Db, B2-Microglobulin, and a 9-Residue Peptide Derived from rat dopamine beta-monooxigenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N5A PDB ENTRY 1N5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 298 ammonium sulphate, Tris HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.3 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.063 α = 90 b = 122.715 β = 103 c = 99.403 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 IMAGE PLATE MARRESEARCH 2000-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.0292 MAX II I711
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 2.7 25 98.8 0.081 14.4 3.5 203819 58548 2 66.2
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) 2.7 2.75 93.6 0.502 2 2.5 2200
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 (All) 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 PDB ENTRY 1N5A 2.7 24.92 53240 53240 2231 100 0.22607 0.226 0.22533 0.2403 0.26176 0.2508 RANDOM 47.366
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] 0.13 -0.08 0.03 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_4_deg 22.946 r_dihedral_angle_3_deg 19.902 r_dihedral_angle_1_deg 6.371 r_scangle_it 2.301 r_scbond_it 1.579 r_angle_refined_deg 1.393 r_mcbond_it 1.172 r_mcangle_it 1.121 r_angle_other_deg 0.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.402 r_dihedral_angle_4_deg 22.946 r_dihedral_angle_3_deg 19.902 r_dihedral_angle_1_deg 6.371 r_scangle_it 2.301 r_scbond_it 1.579 r_angle_refined_deg 1.393 r_mcbond_it 1.172 r_mcangle_it 1.121 r_angle_other_deg 0.795 r_symmetry_vdw_other 0.246 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.204 r_nbd_other 0.197 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_other 0.135 r_symmetry_hbond_refined 0.131 r_mcbond_other 0.108 r_nbtor_other 0.089 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12552 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing