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High resolution structure of the iron Superoxide Dismutase from Thermobifida fusca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BSM 1BSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 25% (w/v) PEG 1500 and
0.1 M sodium malonate dibasic monohydrate, imidazole and boric acid buffer at pH 8.0, from a PACT premier screen
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.61 α = 90 b = 58.59 β = 90 c = 67.94 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 PIXEL DECTRIS PILATUS3 2M 2017-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.25 25 98.79 0.0331 0.998 10.05 5.3 108003 11.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.7 89.74 0.3475 0.673 1.86
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 1BSM 1.25 24.65 1.34 107986 2108 98.77 0.1258 0.1254 0.1254 0.1445 0.1441 16.32
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 12.9505 f_angle_d 1.1326 f_chiral_restr 0.0862 f_bond_d 0.0088 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3201 Nucleic Acid Atoms Solvent Atoms 753 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing