☰ Navigation Tabs
Crystal structure of HLA-DR4 in complex with a mutated human collagen type II peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 290 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.441 α = 90 b = 71.441 β = 90 c = 138.049 γ = 120
Symmetry Space Group P 32 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 2015-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.91842 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 46.07 99 0.087 0.095 0.039 0.999 17.5 11.1 32456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.834 0.913 0.37 0.853 11.5
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 1J8H 1.9 36.951 32382 1564 98.44 0.224 0.2214 0.2217 0.2667 0.2666 35.725
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] 0.14 0.07 0.14 -0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.878 r_dihedral_angle_3_deg 15.723 r_dihedral_angle_4_deg 15.493 r_dihedral_angle_1_deg 8.225 r_lrange_it 4.558 r_lrange_other 4.503 r_scangle_it 1.843 r_scangle_other 1.843 r_angle_refined_deg 1.631 r_mcangle_it 1.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.878 r_dihedral_angle_3_deg 15.723 r_dihedral_angle_4_deg 15.493 r_dihedral_angle_1_deg 8.225 r_lrange_it 4.558 r_lrange_other 4.503 r_scangle_it 1.843 r_scangle_other 1.843 r_angle_refined_deg 1.631 r_mcangle_it 1.525 r_mcangle_other 1.525 r_angle_other_deg 1.293 r_scbond_it 1.158 r_scbond_other 1.157 r_mcbond_it 0.948 r_mcbond_other 0.947 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.189 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.078 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3022 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling XDS data scaling