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Manganese Superoxide Dismutase (Mn-SOD) from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CE4 PDB ENTRY 2CE4 (MONOMER A)
Crystallization Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.577 α = 90 b = 87.1 β = 92.1 c = 116.418 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 41.2 82.2 0.08 31.8 9.4 48281 18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 41.7 0.14 9 7.3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CE4 (MONOMER A) 2 41.2 45779 2483 82 0.176 0.173 0.1866 0.221 RANDOM 22.14
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] 0.48 -0.92 0.51 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.011 r_dihedral_angle_4_deg 16.988 r_dihedral_angle_3_deg 13.426 r_dihedral_angle_1_deg 5.705 r_scangle_it 2.321 r_scbond_it 1.513 r_mcangle_it 1.161 r_angle_refined_deg 1.142 r_angle_other_deg 0.797 r_mcbond_it 0.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.011 r_dihedral_angle_4_deg 16.988 r_dihedral_angle_3_deg 13.426 r_dihedral_angle_1_deg 5.705 r_scangle_it 2.321 r_scbond_it 1.513 r_mcangle_it 1.161 r_angle_refined_deg 1.142 r_angle_other_deg 0.797 r_mcbond_it 0.712 r_nbd_refined 0.201 r_symmetry_vdw_other 0.198 r_symmetry_vdw_refined 0.184 r_nbtor_refined 0.18 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.135 r_nbtor_other 0.085 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6478 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing