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Crystal Structure of HLA B*4405 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 2.52 51.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.64 α = 90 b = 81.62 β = 90 c = 109.65 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 2009-01-22 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 1.9 65.51 100 0.097 19.47 36594 -3 22.147
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 1.9 2 100 0.415 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 1.9 65.51 36594 1830 99.97 0.188 0.186 0.185 0.23 0.2282 RANDOM 20.42
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] 0.01 -0.72 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.071 r_dihedral_angle_4_deg 16.908 r_dihedral_angle_3_deg 13.998 r_dihedral_angle_1_deg 6.002 r_scangle_it 2.264 r_scbond_it 1.486 r_angle_refined_deg 1.251 r_mcangle_it 1.025 r_mcbond_it 0.614 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.071 r_dihedral_angle_4_deg 16.908 r_dihedral_angle_3_deg 13.998 r_dihedral_angle_1_deg 6.002 r_scangle_it 2.264 r_scbond_it 1.486 r_angle_refined_deg 1.251 r_mcangle_it 1.025 r_mcbond_it 0.614 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3171 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 14
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction