☰ Navigation Tabs
Crystal Structure of HLA B*4405 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 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.247 α = 90 b = 81.91 β = 90 c = 109.401 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 2009-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 1 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 1.84 65.51 88.7 0.063 14.5 4.3 35235
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 1.84 1.88 90.6 0.376 4 1759
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 1.84 65.51 35015 1763 88.22 0.207 0.204 0.2024 0.269 0.2675 RANDOM 25.526
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 -0.71 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.226 r_dihedral_angle_4_deg 18.002 r_dihedral_angle_3_deg 16.129 r_dihedral_angle_1_deg 6.262 r_scangle_it 2.273 r_scbond_it 1.462 r_angle_refined_deg 1.258 r_mcangle_it 0.931 r_mcbond_it 0.601 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.226 r_dihedral_angle_4_deg 18.002 r_dihedral_angle_3_deg 16.129 r_dihedral_angle_1_deg 6.262 r_scangle_it 2.273 r_scbond_it 1.462 r_angle_refined_deg 1.258 r_mcangle_it 0.931 r_mcbond_it 0.601 r_nbtor_refined 0.302 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3173 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction