☰ Navigation Tabs
Crystal Structure of HLA B*4403 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 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.692 α = 90 b = 81.738 β = 90 c = 109.893 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 2 40 92.7 0.071 9.2 2.8 29639
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 2.07 74.5 0.264 2.2 2332
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 2 40 29615 1499 92.16 0.188 0.185 0.1852 0.244 0.2421 RANDOM 26.71
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] -0.81 -1.07 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.095 r_dihedral_angle_4_deg 15.823 r_dihedral_angle_3_deg 14.088 r_dihedral_angle_1_deg 6.228 r_scangle_it 2.275 r_scbond_it 1.478 r_angle_refined_deg 1.251 r_mcangle_it 0.98 r_mcbond_it 0.613 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.095 r_dihedral_angle_4_deg 15.823 r_dihedral_angle_3_deg 14.088 r_dihedral_angle_1_deg 6.228 r_scangle_it 2.275 r_scbond_it 1.478 r_angle_refined_deg 1.251 r_mcangle_it 0.98 r_mcbond_it 0.613 r_nbtor_refined 0.302 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3167 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction