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Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other first crystal form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 31% PEG 3350, 90 mM Magnesium Sulfate, 90 mM Sodium Acetate (pH 5.5) 100 mM LiCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.31 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.02 α = 90 b = 69.02 β = 90 c = 108.47 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 MARMOSAIC 300 mm CCD 2010-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.03318 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 50 99.7 0.053 22.61 7 18817 -3 67.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.62 100 0.522 4 7.1
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 MR THROUGHOUT first crystal form 2.55 50 18789 963 0.189 0.186 0.1941 0.239 0.2378 RANDOM 57.29
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] 7.36 7.36 -14.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.118 r_dihedral_angle_4_deg 20.515 r_dihedral_angle_3_deg 16.897 r_dihedral_angle_1_deg 4.798 r_angle_refined_deg 1.845 r_scangle_it 1.493 r_scbond_it 0.941 r_mcangle_it 0.695 r_mcbond_it 0.372 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.118 r_dihedral_angle_4_deg 20.515 r_dihedral_angle_3_deg 16.897 r_dihedral_angle_1_deg 4.798 r_angle_refined_deg 1.845 r_scangle_it 1.493 r_scbond_it 0.941 r_mcangle_it 0.695 r_mcbond_it 0.372 r_chiral_restr 0.124 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2231 Nucleic Acid Atoms 1538 Solvent Atoms 22 Heterogen Atoms 2
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling