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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 1N0J PDB ENTRY 1N0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.2 291 2.7M ammonium sulphate, 0.1M bicine, pH9.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.78 α = 90 b = 81.78 β = 90 c = 136.031 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 1.7 44.07 96.2 0.076 0.076 5 3.7 51295 49346 21.4
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 1.7 1.79 95.8 0.364 0.364 2.9 3.6 7335
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 1N0J 1.7 44.07 51295 49346 2502 95.82 0.1912 0.1912 0.18936 0.1901 0.22596 0.2254 RANDOM 19.396
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] 0.06 0.06 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.043 r_dihedral_angle_4_deg 11.874 r_dihedral_angle_3_deg 11.321 r_dihedral_angle_1_deg 4.43 r_scangle_it 3.029 r_scbond_it 2.022 r_angle_refined_deg 1.398 r_mcangle_it 1.149 r_mcbond_it 0.855 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.043 r_dihedral_angle_4_deg 11.874 r_dihedral_angle_3_deg 11.321 r_dihedral_angle_1_deg 4.43 r_scangle_it 3.029 r_scbond_it 2.022 r_angle_refined_deg 1.398 r_mcangle_it 1.149 r_mcbond_it 0.855 r_nbtor_refined 0.307 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3138 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing