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X-ray structure of mouse interleukin-10 mutant - S1_E8del, C149Y
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 Crystals grew at 20-30% (v/v) glycerolethoxylate, 0.2M ammonium acetate, 0.1M MES (pH 6.3 - 6.8). Crystals appeared after 1-2 days and reached their final size after 3-4 days.
Crystal Properties Matthews coefficient Solvent content 1.77 30.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.77 α = 90 b = 80.82 β = 90 c = 84.32 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD 2012-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2.05 42.15 100 0.083 12.3 4.8 17734
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 2.05 2.16 99.9 0.556 2.9 4.8
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 1LK3 2.05 42.15 16785 902 99.92 0.1911 0.18816 0.197 0.24632 0.2481 RANDOM 38.334
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] -0.34 -1.57 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.87 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_3_deg 15.981 r_long_range_B_refined 8.329 r_long_range_B_other 8.304 r_scangle_other 6.655 r_dihedral_angle_1_deg 5.36 r_mcangle_it 4.302 r_mcangle_other 4.301 r_scbond_it 4.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.87 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_3_deg 15.981 r_long_range_B_refined 8.329 r_long_range_B_other 8.304 r_scangle_other 6.655 r_dihedral_angle_1_deg 5.36 r_mcangle_it 4.302 r_mcangle_other 4.301 r_scbond_it 4.217 r_scbond_other 4.215 r_mcbond_other 3.101 r_mcbond_it 3.099 r_angle_refined_deg 1.548 r_angle_other_deg 0.864 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 2329 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing Coot model building