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Crystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Mn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 58% MPD, 200 mM CaCl2, and 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.65 α = 90 b = 162.65 β = 90 c = 44 γ = 90
Symmetry Space Group P 41 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 PILATUS 6M-F 2012-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97909 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 45.15 99.98 0.999 26.24 34.8 35121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.175 0.881 3.54
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 1dt0 2.1 45.15 33410 1764 99.84 0.17404 0.17303 0.1867 0.19255 0.2014 RANDOM 38.742
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] -0.07 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_3_deg 11.892 r_dihedral_angle_4_deg 6.794 r_dihedral_angle_1_deg 6.028 r_long_range_B_refined 4.458 r_long_range_B_other 4.392 r_scangle_other 3.047 r_scbond_it 1.906 r_scbond_other 1.906 r_mcangle_it 1.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_3_deg 11.892 r_dihedral_angle_4_deg 6.794 r_dihedral_angle_1_deg 6.028 r_long_range_B_refined 4.458 r_long_range_B_other 4.392 r_scangle_other 3.047 r_scbond_it 1.906 r_scbond_other 1.906 r_mcangle_it 1.869 r_mcangle_other 1.869 r_angle_refined_deg 1.282 r_mcbond_it 1.269 r_mcbond_other 1.268 r_angle_other_deg 1.163 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3106 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing