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The C2 Crystal form of SodCI Superoxide Dismutase at 1.7 A resolution with 6 molecules in the asymmetric unit.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300 20 mg/ml SODC1 plus 1.2 mM trachaeal cytotoxin in 20 mM Tris pH 6.6 150 mM NaCl set up as hanging drop with mother liquor Bis-Tris 0.05M, Ammonium Sulfate 0.05M, 30% Pentaerythritol ethoxylate (15/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.838 α = 90 b = 69.474 β = 116.888 c = 95.288 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 PIXEL DECTRIS EIGER X 9M 2019-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07812 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.528 84.987 79.5 0.062 0.067 0.026 0.998 14.4 6.6 187907 19.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.528 1.639 21 0.598 0.671 0.297 0.768 1.7 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6D52 1.7 35.88 1.39 187907 3497 97.69 0.1792 0.1785 0.1877 0.2189 0.219 24.1
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.7949 f_angle_d 1.0306 f_chiral_restr 0.0538 f_bond_d 0.008 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6816 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 32
Software Software Software Name Purpose autoPROC data processing XDS data reduction STARANISO data scaling PHENIX phasing PHENIX refinement