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Murine class I major histocompatibility complex H-2 Db in complex with self-antigen derived from dopamine monooxygenase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.5-2.0M ammonium sulfate
0.1M TRIS HCL, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.07 59.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.245 α = 90 b = 123.597 β = 103.07 c = 99.262 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 PIXEL DECTRIS PILATUS3 6M 2011-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 50 94.5 0.059 0.059 0.998 8.2 2.4 135709 56263
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 95.9 0.427 0.64 1.5
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 1s7u 2.7 45 53380 2843 94.3 0.23562 0.23407 0.2371 0.26441 0.261 RANDOM 82.239
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] -2.01 1.79 2.57 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.492 r_dihedral_angle_4_deg 23.028 r_dihedral_angle_3_deg 20.61 r_long_range_B_refined 13.714 r_long_range_B_other 13.714 r_mcangle_it 10.213 r_mcangle_other 10.213 r_scangle_other 9.889 r_dihedral_angle_1_deg 7.347 r_mcbond_it 6.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.492 r_dihedral_angle_4_deg 23.028 r_dihedral_angle_3_deg 20.61 r_long_range_B_refined 13.714 r_long_range_B_other 13.714 r_mcangle_it 10.213 r_mcangle_other 10.213 r_scangle_other 9.889 r_dihedral_angle_1_deg 7.347 r_mcbond_it 6.515 r_mcbond_other 6.515 r_scbond_it 6.253 r_scbond_other 6.252 r_angle_refined_deg 1.522 r_angle_other_deg 1.109 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 12632 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing