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Structure of HLA-A2 in complex with D76N b2m mutant and NY-ESO1 double mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9W PDB entry 1S9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.9 M ammonium sulphate, 2% PEG 6K, 100 mM Tris-HCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.03 69.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.11 α = 90 b = 314.5 β = 90 c = 316.23 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 110 CCD ADSC QUANTUM 315r 2012-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 2.64 70.63 99.7 0.168 6.8 5.3 294283 293400
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 2.64 2.79 99.7 0.905 1.9 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1S9W 2.64 66.48 278467 14628 97.72 0.2001 0.19914 0.2062 0.21834 0.2243 RANDOM 38.669
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] -19.43 12.51 6.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.844 r_dihedral_angle_4_deg 19.598 r_dihedral_angle_3_deg 16.637 r_dihedral_angle_1_deg 6.257 r_scangle_it 2.501 r_scbond_it 1.445 r_mcangle_it 1.253 r_angle_refined_deg 1.218 r_angle_other_deg 0.796 r_mcbond_it 0.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.844 r_dihedral_angle_4_deg 19.598 r_dihedral_angle_3_deg 16.637 r_dihedral_angle_1_deg 6.257 r_scangle_it 2.501 r_scbond_it 1.445 r_mcangle_it 1.253 r_angle_refined_deg 1.218 r_angle_other_deg 0.796 r_mcbond_it 0.651 r_mcbond_other 0.092 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 44422 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 158
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling