☰ Navigation Tabs
Crystal Structure of HLA B*4402 in complex with EEYLKAWTF, a mimotope
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 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.705 α = 90 b = 81.868 β = 90 c = 109.814 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1 APS 23-ID-D
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 1.6 100 93.4 0.067 21.4 3.8 57027
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 1.6 1.66 99 0.472 3.8 5975
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 1.6 65.65 56266 2847 92.1 0.203 0.201 0.2037 0.241 0.1961 RANDOM 26.176
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] -1.06 -0.61 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.985 r_dihedral_angle_4_deg 16.196 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_1_deg 5.728 r_scangle_it 2.268 r_scbond_it 1.532 r_angle_refined_deg 1.202 r_mcangle_it 1.008 r_mcbond_it 0.617 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.985 r_dihedral_angle_4_deg 16.196 r_dihedral_angle_3_deg 12.931 r_dihedral_angle_1_deg 5.728 r_scangle_it 2.268 r_scbond_it 1.532 r_angle_refined_deg 1.202 r_mcangle_it 1.008 r_mcbond_it 0.617 r_nbtor_refined 0.303 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.119 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3169 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction