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Crystal structure of HLA-B*35:01-NP9 epitope from 2006 H1N1 influenza strain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LKS 3LKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 PEG, Acetate
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.919 α = 90 b = 81.737 β = 90 c = 109.417 γ = 90
Symmetry Space Group P 21 21 21
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 2019-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.75 24.8 100 0.042 0.999 17.8 2 46767 16.9172395997
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 1.75 1.81 0.326 0.888 3.5
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 3LKS 1.75002880736 24.797072884 1.35597307965 46757 2341 99.8846424986 0.173853733974 0.171749861358 0.1755 0.213573953668 0.2146 23.9992744442
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 19.093111476 f_angle_d 1.51925308469 f_chiral_restr 0.114395975595 f_bond_d 0.0134792676746 f_plane_restr 0.0100539489728
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3162 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing