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Crystal structure of HLA-DR4 in complex with a HSP70 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 0.03 M of each divalent cation (12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD), 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.23 α = 90 b = 76.23 β = 90 c = 170.66 γ = 90
Symmetry Space Group P 43 2 2
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 2016-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 2.24 56.89 99.8 0.237 0.246 0.066 0.999 12 25.6 25047
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 2.24 2.31 3.474 3.605 0.961 0.635 26.6
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 (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 2.24 51.453 22463 1105 89.691 0.201 0.1985 0.1985 0.2422 0.2424 53.581
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] -0.036 -0.036 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.629 r_dihedral_angle_3_deg 19.352 r_dihedral_angle_4_deg 17.579 r_dihedral_angle_1_deg 8.263 r_lrange_it 5.844 r_lrange_other 5.826 r_scangle_it 4.008 r_scangle_other 4.007 r_mcangle_it 2.809 r_mcangle_other 2.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.629 r_dihedral_angle_3_deg 19.352 r_dihedral_angle_4_deg 17.579 r_dihedral_angle_1_deg 8.263 r_lrange_it 5.844 r_lrange_other 5.826 r_scangle_it 4.008 r_scangle_other 4.007 r_mcangle_it 2.809 r_mcangle_other 2.808 r_scbond_it 2.486 r_scbond_other 2.484 r_mcbond_it 1.764 r_mcbond_other 1.764 r_angle_refined_deg 1.659 r_angle_other_deg 1.213 r_symmetry_xyhbond_nbd_refined 0.228 r_symmetry_nbd_refined 0.201 r_nbd_refined 0.199 r_nbd_other 0.19 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.174 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3057 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction XDS data scaling