☰ Navigation Tabs
Crystal structure of HLA-DR4 in complex with a human collagen type II peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 290 20% polyethylene glycol 3350 and 200 mM ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.86 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.418 α = 90 b = 71.84 β = 111.331 c = 125.721 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.05 47.009 98.1 0.999 8.2 1 62583
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 0.851 1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6BIL 2.05 47.009 62583 3061 97.882 0.194 0.192 0.1931 0.2449 0.2482 46.285
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] -0.63 -0.378 0.592 0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.774 r_dihedral_angle_4_deg 20.232 r_dihedral_angle_3_deg 16.161 r_dihedral_angle_1_deg 8.377 r_lrange_it 5.653 r_lrange_other 5.58 r_scangle_it 3.063 r_scangle_other 3.062 r_mcangle_it 2.396 r_mcangle_other 2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.774 r_dihedral_angle_4_deg 20.232 r_dihedral_angle_3_deg 16.161 r_dihedral_angle_1_deg 8.377 r_lrange_it 5.653 r_lrange_other 5.58 r_scangle_it 3.063 r_scangle_other 3.062 r_mcangle_it 2.396 r_mcangle_other 2.396 r_scbond_it 1.911 r_scbond_other 1.911 r_angle_refined_deg 1.844 r_mcbond_it 1.528 r_mcbond_other 1.528 r_angle_other_deg 1.318 r_symmetry_nbd_refined 0.415 r_nbd_other 0.268 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6330 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC data reduction REFMAC refinement xia2 data reduction Aimless data scaling