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Crystal Structure of HLA B*3501 in complex with influenza NP418 epitope from 1972 strain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FYY pdb entry 2FYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 15-25% PEG 4000, 0.2M NH4Acetate, 0.1M Na-Citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.12 α = 90 b = 82.02 β = 90 c = 110.43 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 210r 2009-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 1.0000 Australian Synchrotron MX1
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 1.8 65.84 99.8 0.082 15.78 44107 -3 27.136
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) 1.8 1.9 99.9 0.685 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 pdb entry 2FYY 1.8 65.84 43749 2201 99.79 0.212 0.211 0.2157 0.244 0.2491 RANDOM 22.636
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] -0.73 -0.87 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 19.331 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 6.156 r_scangle_it 3.329 r_scbond_it 2.068 r_angle_refined_deg 1.388 r_mcangle_it 1.373 r_mcbond_it 0.763 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 19.331 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 6.156 r_scangle_it 3.329 r_scbond_it 2.068 r_angle_refined_deg 1.388 r_mcangle_it 1.373 r_mcbond_it 0.763 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3164 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Bue data collection XDS data reduction