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Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JK8 PDB ENTRIES 1JK8 and 1S9V experimental model PDB 1S9V PDB ENTRIES 1JK8 and 1S9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2M Li2So4, 0.1M Tris, 30% PEG 4000, 8% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.89 α = 90 b = 114.92 β = 103.36 c = 138.03 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 CCD MARMOSAIC 325 mm CCD Mirrors 2009-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.05 29.31 0.068 16.4 4.2 21713 21713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.13 99.6 0.851 1.9 4.2 1629
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 (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 ENTRIES 1JK8 and 1S9V 3.05 29.31 21713 20626 1086 100 0.21398 0.21045 0.2149 0.28321 0.2863 RANDOM 91.852
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] 4.86 -9.39 -1.81 -7.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_3_deg 20.733 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_1_deg 7.363 r_scangle_it 1.864 r_angle_refined_deg 1.393 r_scbond_it 1.047 r_mcangle_it 1.03 r_mcbond_it 0.552 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_3_deg 20.733 r_dihedral_angle_4_deg 15.752 r_dihedral_angle_1_deg 7.363 r_scangle_it 1.864 r_angle_refined_deg 1.393 r_scbond_it 1.047 r_mcangle_it 1.03 r_mcbond_it 0.552 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 6102 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 12
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling