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Crystal structure of SLE patient-derived anti-DNA antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG 8000, 0.1M Phosphate-citrate (pH 4.2), 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.356 α = 90 b = 41.167 β = 113.07 c = 155.996 γ = 90
Symmetry Space Group C 1 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 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 2.05 50 99.9 0.083 22.8 4.4 52059
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 2.05 2.1 100 0.619 2.3 4.3
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 5GKR 2.05 29.65 49440 2618 99.82 0.21935 0.21745 0.2222 0.25534 0.262 RANDOM 36.078
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] 1 -1.08 -1.97 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 17.681 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_1_deg 7.462 r_long_range_B_refined 3.933 r_long_range_B_other 3.907 r_angle_refined_deg 1.453 r_angle_other_deg 0.904 r_mcangle_it 0.53 r_mcangle_other 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 17.681 r_dihedral_angle_3_deg 13.053 r_dihedral_angle_1_deg 7.462 r_long_range_B_refined 3.933 r_long_range_B_other 3.907 r_angle_refined_deg 1.453 r_angle_other_deg 0.904 r_mcangle_it 0.53 r_mcangle_other 0.53 r_scangle_other 0.371 r_mcbond_it 0.291 r_mcbond_other 0.291 r_scbond_it 0.228 r_scbond_other 0.206 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 6227 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing