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Crystal Structure of HLA B*4402 in complex with EEYLQAFTY a self peptide from the ABCD3 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SYV PDB ENTRY 1SYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 0.2M ammonium acetate, 20-28% PEG 4000, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.79 α = 90 b = 81.7 β = 90 c = 109.9 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9 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 1.95 46.109 87.8 0.051 11.13 29968 -3 22.883
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 1.95 2 68.4 0.114 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SYV 1.96 15 29906 3001 89.07 0.205 0.2 0.2019 0.253 0.2539 RANDOM 11.86
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_3_deg 15.649 r_dihedral_angle_1_deg 6.172 r_scangle_it 1.942 r_scbond_it 1.28 r_angle_refined_deg 1.175 r_mcangle_it 0.901 r_mcbond_it 0.605 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.751 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_3_deg 15.649 r_dihedral_angle_1_deg 6.172 r_scangle_it 1.942 r_scbond_it 1.28 r_angle_refined_deg 1.175 r_mcangle_it 0.901 r_mcbond_it 0.605 r_nbtor_refined 0.305 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3167 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction