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Crystal Structure of HLA class II major histocompatibility complex bound to HCMV-IE1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 16% w/v PEG 8000, 40 mM potassium dihydrogen phosphate, and 20% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.7 54.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.27 α = 90 b = 96.18 β = 92.66 c = 160.09 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 CCD ADSC QUANTUM 315r 2024-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9537 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.426 48.09 99.8 0.103 0.99 14.98 7.01 81784 51.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.45 99.2 1.192 0.765 1.5 6.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.426 35.3 81764 4089 99.8 0.2256 0.2247 0.2116 0.2436 0.2331 RANDOM 62.94
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] -12.0796 14.4533 9.8746 2.205
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.67 t_omega_torsion 3.25 t_angle_deg 0.87 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12534 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 81
Software Software Software Name Purpose BUSTER refinement XDS data reduction PHASER phasing MxCuBE data collection Coot model building