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Crystal Structure of Manganese Superoxide Dismutase from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VEW PDB ENTRY 1VEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 298 200mM ammonium acetate (pH 7.1) 20%(w/v) PEG3350, 0.3M NaCl, 0.3M imidazole, 20mM Tris (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.801 α = 90 b = 87.922 β = 91.14 c = 116.198 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2004-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.1 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 119.5 99.8 0.074 15.4 3.7 74526 74526 31.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.92 99.8 0.493 2.6 3.5 7437
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VEW 1.853 119.523 74526 74526 3697 99.559 0.185 0.185 0.1841 0.1824 0.205 0.2048 RANDOM 31.125
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] 1.903 -1.797 -0.959 -1.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.443 r_dihedral_angle_3_deg 12.946 r_dihedral_angle_4_deg 12.197 r_dihedral_angle_1_deg 5.212 r_scangle_it 2.279 r_scbond_it 1.446 r_angle_refined_deg 1.093 r_mcangle_it 0.862 r_mcbond_it 0.54 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.443 r_dihedral_angle_3_deg 12.946 r_dihedral_angle_4_deg 12.197 r_dihedral_angle_1_deg 5.212 r_scangle_it 2.279 r_scbond_it 1.446 r_angle_refined_deg 1.093 r_mcangle_it 0.862 r_mcbond_it 0.54 r_nbtor_refined 0.298 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.141 r_symmetry_hbond_refined 0.117 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.084 r_metal_ion_refined 0.025 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6565 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing