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HLA-DR1 with GMF Influenza PB1 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 Seeded with DR1-QAR crystals. 0.2M LiCl, 20% PEG 6K, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 4.67 73.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.017 α = 90 b = 184.017 β = 90 c = 87.285 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 PILATUS3 S 6M 2017-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97265 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.086 92.02 100 0.191 0.201 0.06 10.3 11 31506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.086 3.17 100 3.078 3.231 0.979 10.9
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 3.09 92.008 31427 1532 99.557 0.185 0.1834 0.1852 0.2259 0.2297 81.326
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] -0.148 -0.074 -0.148 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.735 r_dihedral_angle_3_deg 20.243 r_dihedral_angle_4_deg 17.646 r_dihedral_angle_1_deg 7.725 r_lrange_it 6.25 r_scangle_it 3.963 r_mcangle_it 2.932 r_scbond_it 2.384 r_mcbond_it 1.697 r_angle_refined_deg 1.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.735 r_dihedral_angle_3_deg 20.243 r_dihedral_angle_4_deg 17.646 r_dihedral_angle_1_deg 7.725 r_lrange_it 6.25 r_scangle_it 3.963 r_mcangle_it 2.932 r_scbond_it 2.384 r_mcbond_it 1.697 r_angle_refined_deg 1.681 r_nbtor_refined 0.322 r_symmetry_xyhbond_nbd_refined 0.265 r_symmetry_nbd_refined 0.242 r_nbd_refined 0.238 r_ncsr_local_group_3 0.171 r_xyhbond_nbd_refined 0.137 r_ncsr_local_group_1 0.131 r_chiral_restr 0.121 r_ncsr_local_group_2 0.114 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6148 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling Aimless data scaling PHASER phasing