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Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QHK 4QHK, 4Y5Y, 4IDJ, and 4LLW experimental model PDB 4Y5Y 4QHK, 4Y5Y, 4IDJ, and 4LLW experimental model PDB 4IDJ 4QHK, 4Y5Y, 4IDJ, and 4LLW experimental model PDB 4LLW 4QHK, 4Y5Y, 4IDJ, and 4LLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris-HCl (pH 7.0), 0.2 M NaCl, 1 M Sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.515 α = 90 b = 147.515 β = 90 c = 112.807 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2015-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 50 100 0.115 23.1 5.8 53509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.857 2.6 5.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4QHK, 4Y5Y, 4IDJ, and 4LLW 2.1 26.33 50879 2609 99.98 0.16359 0.16253 0.18512 0.1791 RANDOM 39.752
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] -2.08 -2.08 4.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.268 r_dihedral_angle_4_deg 13.916 r_dihedral_angle_3_deg 13.369 r_dihedral_angle_1_deg 6.646 r_long_range_B_refined 2.927 r_long_range_B_other 2.927 r_angle_refined_deg 1.295 r_angle_other_deg 1.051 r_mcangle_it 0.961 r_mcangle_other 0.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.268 r_dihedral_angle_4_deg 13.916 r_dihedral_angle_3_deg 13.369 r_dihedral_angle_1_deg 6.646 r_long_range_B_refined 2.927 r_long_range_B_other 2.927 r_angle_refined_deg 1.295 r_angle_other_deg 1.051 r_mcangle_it 0.961 r_mcangle_other 0.961 r_scangle_other 0.882 r_mcbond_it 0.545 r_mcbond_other 0.545 r_scbond_it 0.515 r_scbond_other 0.508 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6239 Nucleic Acid Atoms 64 Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing