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HLA-DR1 with SGP Influenza Matrix 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 7.5 291 0.1 M Tris
0.2 M NH4 SO4
25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.42 α = 90 b = 76.73 β = 93.5 c = 90.13 γ = 90
Symmetry Space Group P 1 21 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 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) 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 2.66 55.54 99.1 0.196 0.229 0.116 6.3 3.7 26304
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 2.66 2.73 98.7 1.043 1.215 0.616 0.466 1.5
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 1DLH 2.66 55.537 26290 1267 98.95 0.203 0.2001 0.2021 0.2539 0.2599 42.325
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] -2.441 0.044 -0.072 2.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.351 r_dihedral_angle_4_deg 21.793 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_1_deg 7.858 r_lrange_it 4.913 r_scangle_it 2.228 r_mcangle_it 1.989 r_angle_refined_deg 1.684 r_scbond_it 1.373 r_mcbond_it 1.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.351 r_dihedral_angle_4_deg 21.793 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_1_deg 7.858 r_lrange_it 4.913 r_scangle_it 2.228 r_mcangle_it 1.989 r_angle_refined_deg 1.684 r_scbond_it 1.373 r_mcbond_it 1.134 r_nbtor_refined 0.317 r_symmetry_nbd_refined 0.245 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.176 r_ncsr_local_group_3 0.164 r_symmetry_xyhbond_nbd_refined 0.142 r_chiral_restr 0.127 r_ncsr_local_group_1 0.098 r_ncsr_local_group_2 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6262 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data scaling Aimless data scaling PHASER phasing