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Crystal structure of HLA-DRA*01:01/HLA-DRB1*04:01 in complex with c44H10 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLH 1DLH, 1AJ7 experimental model PDB 1AJ7 1DLH, 1AJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.7 M ammonium sulfate, 15% glycerol, 0.085 M HEPES, 1.7% PEG400, with crystal seeds previously grown in 2 M ammonium sulfate, 0.1 M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.62 66.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.15 α = 90 b = 178.72 β = 90 c = 182.04 γ = 90
Symmetry Space Group I 2 2 2
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 EIGER X 16M 2022-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 3.09 40 99.9 0.159 0.041 0.99 14.8 16.1 50733
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.09 3.14 99.9 0.878 0.226 0.709 1.5 16.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DLH, 1AJ7 3.09 39.51 1.35 50691 1995 99.91 0.2018 0.2001 0.2009 0.2438 0.2431 105.25
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.2791 f_angle_d 0.7185 f_chiral_restr 0.0451 f_plane_restr 0.0049 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12889 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing