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Crystal Structure of a manganese superoxide dismutases from Caenorhabditis elegans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DC5 C. Elegans MnSOD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.2 291 3M ammonium sulphate, 0.1M bicine, pH9.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.98 α = 90 b = 80.98 β = 90 c = 137.444 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 CCD ADSC QUANTUM 315 mirrors 2007-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.060 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 69.84 97.2 0.056 0.056 8.7 4.2 42770 41573 17.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 98.9 0.144 0.144 8.5 4.2 6162
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT C. Elegans MnSOD3 1.8 43.99 42770 41573 2105 96.35 0.17079 0.17079 0.1692 0.1705 0.20121 0.2008 RANDOM 15.646
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] -0.31 -0.31 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_3_deg 11.573 r_dihedral_angle_1_deg 5.054 r_dihedral_angle_4_deg 4.469 r_scangle_it 2.317 r_scbond_it 1.472 r_angle_refined_deg 1.109 r_mcangle_it 0.837 r_mcbond_it 0.605 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_3_deg 11.573 r_dihedral_angle_1_deg 5.054 r_dihedral_angle_4_deg 4.469 r_scangle_it 2.317 r_scbond_it 1.472 r_angle_refined_deg 1.109 r_mcangle_it 0.837 r_mcbond_it 0.605 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.138 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3105 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling