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Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5
10% (vol/vol) MPD
15% (vol/vol) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.606 α = 90 b = 128.319 β = 90 c = 53.521 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 2M 2016-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 46.86 98.9 0.996 9.9 4.4 103630 23.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NI9 1.35 46.86 101530 2100 98.87 0.14281 0.14201 0.1425 0.1808 0.1811 RANDOM 22.68
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] 0.73 -1.18 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.07 r_sphericity_free 25.552 r_dihedral_angle_4_deg 16.776 r_dihedral_angle_3_deg 11.401 r_sphericity_bonded 9.525 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 3.543 r_long_range_B_other 3.542 r_scangle_other 2.687 r_scbond_it 2.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.07 r_sphericity_free 25.552 r_dihedral_angle_4_deg 16.776 r_dihedral_angle_3_deg 11.401 r_sphericity_bonded 9.525 r_dihedral_angle_1_deg 6.796 r_long_range_B_refined 3.543 r_long_range_B_other 3.542 r_scangle_other 2.687 r_scbond_it 2.194 r_scbond_other 2.192 r_rigid_bond_restr 2.178 r_mcangle_it 2.161 r_mcangle_other 2.16 r_mcbond_it 1.716 r_mcbond_other 1.715 r_angle_refined_deg 1.55 r_angle_other_deg 0.924 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3217 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing