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Synthetic glycoform of Human Interleukin 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ALU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2-0.25 M sodium malonate, pH 7.0 and 18-22% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.1 α = 90 b = 129.02 β = 90 c = 50.1 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 PILATUS3 6M 2015-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918007 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.998 50 98.2 0.07 0.084 0.999 10.62 3.22 16028 46.024
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.998 2.12 95.9 1.412 1.67 0.434 0.72 3.38
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 1alu 1.998 39.569 16028 802 98.622 0.209 0.2063 0.2064 0.2526 0.2529 52.097
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] 2.71 -1.547 -1.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.386 r_dihedral_angle_4_deg 21.345 r_dihedral_angle_3_deg 16.337 r_lrange_it 6.89 r_lrange_other 6.703 r_dihedral_angle_1_deg 5.378 r_scangle_it 4.214 r_scangle_other 4.214 r_mcangle_other 3.264 r_mcangle_it 3.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.386 r_dihedral_angle_4_deg 21.345 r_dihedral_angle_3_deg 16.337 r_lrange_it 6.89 r_lrange_other 6.703 r_dihedral_angle_1_deg 5.378 r_scangle_it 4.214 r_scangle_other 4.214 r_mcangle_other 3.264 r_mcangle_it 3.247 r_scbond_it 2.749 r_scbond_other 2.745 r_mcbond_it 2.113 r_mcbond_other 2.071 r_angle_refined_deg 1.647 r_angle_other_deg 1.351 r_nbd_other 0.23 r_nbd_refined 0.207 r_symmetry_nbd_refined 0.202 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1233 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing