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Crystal structure of HLA-DR4 presenting citrullinated Tenascin C peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.2 M NaCl, 0.1 M Bis Tris pH 5.5, 29% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.3 α = 90 b = 119.3 β = 90 c = 73.273 γ = 120
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 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 34.53 99.6 0.092 0.102 0.045 0.998 16.4 10.2 15161 38.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.3 0.352 0.391 0.17 0.97 7.2 10.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 34.53 2.07 15153 786 99.58 0.186 0.1842 0.1842 0.2186 0.218 44.39
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 7.3763 f_angle_d 0.6914 f_chiral_restr 0.045 f_plane_restr 0.0054 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3076 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing