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Crystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Fe
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 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.79 α = 90 b = 162.79 β = 90 c = 43.84 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 57.62 99.85 0.942 17.11 122 40497
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 2.072 100 0.833 3.37
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 57.62 38414 2027 99.86 0.1696 0.1686 0.1801 0.1882 0.195 RANDOM 33.514
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] 0.59 0.59 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.691 r_dihedral_angle_3_deg 12.373 r_dihedral_angle_1_deg 6.132 r_dihedral_angle_4_deg 5.296 r_long_range_B_refined 3.819 r_long_range_B_other 3.72 r_scangle_other 1.834 r_scbond_other 1.483 r_scbond_it 1.482 r_angle_refined_deg 1.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.691 r_dihedral_angle_3_deg 12.373 r_dihedral_angle_1_deg 6.132 r_dihedral_angle_4_deg 5.296 r_long_range_B_refined 3.819 r_long_range_B_other 3.72 r_scangle_other 1.834 r_scbond_other 1.483 r_scbond_it 1.482 r_angle_refined_deg 1.422 r_angle_other_deg 1.212 r_mcangle_it 1.1 r_mcangle_other 1.099 r_mcbond_it 0.709 r_mcbond_other 0.709 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3106 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing