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Crystal Structure of H-2Db in complex with a variant M6A of the NP366 peptide from influenza A virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M potassium thiocianate, 30% PEG 2000, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.71 α = 99.95 b = 69.7 β = 111.04 c = 72.38 γ = 110.48
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2008-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.514
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 2.5 50 95 0.094 13.69 2.6 32162 30549 20.343
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) 2.5 2.6 93.9 0.273 5 2.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YN7 2.5 15 30430 3069 95.38 0.227 0.22 0.286 0.2267 RANDOM 14.635
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] -0.36 0.25 0.29 0.26 -0.49 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_3_deg 21.113 r_dihedral_angle_4_deg 20.588 r_dihedral_angle_1_deg 6.916 r_scangle_it 1.663 r_mcangle_it 1.601 r_angle_refined_deg 1.422 r_scbond_it 1.114 r_mcbond_it 0.915 r_symmetry_hbond_refined 0.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_3_deg 21.113 r_dihedral_angle_4_deg 20.588 r_dihedral_angle_1_deg 6.916 r_scangle_it 1.663 r_mcangle_it 1.601 r_angle_refined_deg 1.422 r_scbond_it 1.114 r_mcbond_it 0.915 r_symmetry_hbond_refined 0.402 r_symmetry_vdw_refined 0.342 r_nbtor_refined 0.33 r_nbd_refined 0.274 r_xyhbond_nbd_refined 0.24 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6385 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction