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Crystal Structure of HLA B*3501 in complex with influenza NP418 epitope from 1980 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 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.23 α = 90 b = 82.07 β = 90 c = 110.41 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 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.0000 Australian Synchrotron MX2
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 1.9 65.87 99.6 0.092 17.84 37309 -3 26.189
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) 1.9 2 99.6 0.509 4.4
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 pdb entry 2FYY 1.9 65.87 37309 1866 99.64 0.212 0.21 0.26 0.2455 RANDOM 23.473
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] -0.51 -0.96 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.494 r_dihedral_angle_1_deg 6.27 r_scangle_it 3.436 r_scbond_it 2.092 r_angle_refined_deg 1.44 r_mcangle_it 1.393 r_mcbond_it 0.776 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.494 r_dihedral_angle_1_deg 6.27 r_scangle_it 3.436 r_scbond_it 2.092 r_angle_refined_deg 1.44 r_mcangle_it 1.393 r_mcbond_it 0.776 r_chiral_restr 0.103 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 187 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Bue data collection XDS data reduction