☰ Navigation Tabs
Crystal structure of the Murine class I Major Histocompatibility Complex of H-2DB, 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 1HOC PDB ENTRY 1HOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Ammonium sulfate, ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.08 59.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.998 α = 90 b = 122.657 β = 103.34 c = 99.18 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 2.85 20 92.6 0.096 12 2.9 46560 46560 63.9
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 2.85 2.9 94.4 0.254 9.8 2.9 2453
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 1HOC 2.85 19.92 43227 43227 2277 100 0.2526 0.25264 0.25128 0.2517 0.27861 0.2768 RANDOM 11.109
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] -0.34 -2.6 1.53 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.018 r_dihedral_angle_1_deg 4.38 r_scangle_it 3.298 r_angle_refined_deg 2.282 r_scbond_it 1.912 r_mcangle_it 1.305 r_mcbond_it 0.672 r_symmetry_vdw_refined 0.428 r_symmetry_hbond_refined 0.355 r_nbd_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.018 r_dihedral_angle_1_deg 4.38 r_scangle_it 3.298 r_angle_refined_deg 2.282 r_scbond_it 1.912 r_mcangle_it 1.305 r_mcbond_it 0.672 r_symmetry_vdw_refined 0.428 r_symmetry_hbond_refined 0.355 r_nbd_refined 0.31 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.133 r_bond_refined_d 0.031 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12568 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement