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Crystal structure of the Murine class I Major Histocompatibility Complex of H-2KB, B2-Microglobulin, and A 9-Residue immunodominant peptide epitope gp33 derived from LCMV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OSZ PDB ENTRY 1OSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG8000, magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.02 58.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.551 α = 90 b = 88.574 β = 93.72 c = 120.09 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 120 IMAGE PLATE MARRESEARCH 2000-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.018 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 2.9 20 86.4 0.13 8.4 2.3 46919 46919 43.1
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 2.9 2.95 62.2 0.242 3.5 2.06 733
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 1OSZ 2.95 19.92 18616 18616 986 100 0.2319 0.23195 0.22904 0.2251 0.2868 0.2799 RANDOM 26.531
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] -1.47 4.55 -7.69 9.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.087 r_scangle_it 3.699 r_dihedral_angle_1_deg 2.822 r_scbond_it 2.158 r_mcangle_it 1.792 r_angle_refined_deg 1.761 r_mcbond_it 0.935 r_symmetry_hbond_refined 0.401 r_nbd_refined 0.307 r_symmetry_vdw_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.087 r_scangle_it 3.699 r_dihedral_angle_1_deg 2.822 r_scbond_it 2.158 r_mcangle_it 1.792 r_angle_refined_deg 1.761 r_mcbond_it 0.935 r_symmetry_hbond_refined 0.401 r_nbd_refined 0.307 r_symmetry_vdw_refined 0.298 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6260 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement