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HLA-DR1 with the QAR Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 0.1 M Na Cacodylate,
0.2 M NH4 SO4,
20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.06 α = 90 b = 116.08 β = 90 c = 43.68 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 S 6M 2016-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
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 1.64 71.16 99.8 0.094 10.3 7.1 56957
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.68 1.912 0.753 0.518
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 1DLH 1.64 71.156 56904 2819 99.797 0.204 0.2018 0.2081 0.2399 0.2437 36.371
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] -1.414 -1.492 2.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.518 r_dihedral_angle_1_deg 23.335 r_dihedral_angle_4_deg 17.954 r_dihedral_angle_3_deg 14.971 r_dihedral_angle_other_3_deg 11.96 r_lrange_it 6.927 r_lrange_other 6.866 r_scangle_it 2.263 r_scangle_other 2.257 r_angle_refined_deg 1.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.518 r_dihedral_angle_1_deg 23.335 r_dihedral_angle_4_deg 17.954 r_dihedral_angle_3_deg 14.971 r_dihedral_angle_other_3_deg 11.96 r_lrange_it 6.927 r_lrange_other 6.866 r_scangle_it 2.263 r_scangle_other 2.257 r_angle_refined_deg 1.687 r_mcangle_it 1.685 r_mcangle_other 1.685 r_scbond_it 1.47 r_scbond_other 1.467 r_angle_other_deg 1.349 r_mcbond_it 1.063 r_mcbond_other 1.063 r_symmetry_nbd_refined 0.271 r_nbd_other 0.212 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.166 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3135 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling XDS data scaling PHASER phasing