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Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 altered peptide ligand (Y4A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7U PDB ENTRY 1S7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 1.8 M ammonium sulfate, 0.1 M Tris HCl pH 9.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.32 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.51 α = 90 b = 126.21 β = 124.54 c = 96.47 γ = 90
Symmetry Space Group C 1 2 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 MAR scanner 345 mm plate 2004-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.007 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 36.2 98.9 0.052 0.052 20 3.7 44615 44615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 81 0.213 0.213 4.7 3.5 5419
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 PDB ENTRY 1S7U 2.41 33.9 42333 2252 98.98 0.2439 0.24168 0.2484 0.2849 0.2878 RANDOM 56.576
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] -0.16 -0.17 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.023 r_dihedral_angle_4_deg 21.433 r_dihedral_angle_3_deg 17.472 r_dihedral_angle_1_deg 6.065 r_scangle_it 2.39 r_scbond_it 1.406 r_mcangle_it 1.2 r_angle_refined_deg 1.192 r_mcbond_it 0.629 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.023 r_dihedral_angle_4_deg 21.433 r_dihedral_angle_3_deg 17.472 r_dihedral_angle_1_deg 6.065 r_scangle_it 2.39 r_scbond_it 1.406 r_mcangle_it 1.2 r_angle_refined_deg 1.192 r_mcbond_it 0.629 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6090 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling