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Crystal structure of HLA-DR4 in complex with a citrullinated cilp peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 290 0.1M sodium acetate trihydrate pH 5.5, 0.2M lithium chloride, 18% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.277 α = 90 b = 112.244 β = 90 c = 212.981 γ = 90
Symmetry Space Group C 2 2 21
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 2016-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9763 ESRF ID23-1
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 2.83 56.12 98.6 0.151 0.164 0.061 0.998 14.4 13.3 27807
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 2.83 2.98 1.617 1.749 0.659 0.612 13.2
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 6BIL 2.831 49.698 27756 1402 98.457 0.246 0.2445 0.2444 0.2833 0.2835 89.442
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] -0.283 -1.032 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.111 r_dihedral_angle_4_deg 18.103 r_dihedral_angle_3_deg 15.653 r_dihedral_angle_1_deg 9.232 r_lrange_it 9.21 r_lrange_other 9.21 r_scangle_it 4.376 r_scangle_other 4.376 r_mcangle_it 3.389 r_mcangle_other 3.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.111 r_dihedral_angle_4_deg 18.103 r_dihedral_angle_3_deg 15.653 r_dihedral_angle_1_deg 9.232 r_lrange_it 9.21 r_lrange_other 9.21 r_scangle_it 4.376 r_scangle_other 4.376 r_mcangle_it 3.389 r_mcangle_other 3.389 r_scbond_it 2.623 r_scbond_other 2.623 r_mcbond_it 2.089 r_mcbond_other 2.085 r_angle_refined_deg 1.622 r_angle_other_deg 1.381 r_symmetry_xyhbond_nbd_other 0.509 r_symmetry_nbd_refined 0.421 r_ext_dist_refined_d 0.312 r_nbd_other 0.228 r_xyhbond_nbd_refined 0.226 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.171 r_ncsr_local_group_2 0.096 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_1 0.082 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_bond_other_d 0.011 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6252 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling