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The crystal structure of human interleukin-11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ALU pdb entry 1ALU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 1.25 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M bis-tris propane, 10% formamide, 0.02% sodium azide, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.83 32.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.862 α = 90 b = 28.169 β = 90 c = 41.806 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315r 2012-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.09 41.81 99.6 0.09 0.12 11.5 3.8 8862 29.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.15 97.5 0.459 0.611 2.9 3.8 648
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 pdb entry 1ALU 2.09 41.81 8203 624 99.52 0.18855 0.18435 0.24155 0.213 RANDOM 29.419
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] 2.53 -1.01 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.202 r_dihedral_angle_4_deg 18.935 r_dihedral_angle_3_deg 14.645 r_long_range_B_refined 6.103 r_long_range_B_other 6 r_dihedral_angle_1_deg 5.143 r_mcangle_it 2.943 r_mcangle_other 2.942 r_scangle_other 2.645 r_mcbond_it 1.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.202 r_dihedral_angle_4_deg 18.935 r_dihedral_angle_3_deg 14.645 r_long_range_B_refined 6.103 r_long_range_B_other 6 r_dihedral_angle_1_deg 5.143 r_mcangle_it 2.943 r_mcangle_other 2.942 r_scangle_other 2.645 r_mcbond_it 1.678 r_mcbond_other 1.678 r_scbond_it 1.538 r_scbond_other 1.537 r_angle_refined_deg 1.389 r_angle_other_deg 0.797 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 1214 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction Aimless data scaling