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Native human manganese superoxide dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 296 1.8 M Potassium Phosphate, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.24 α = 90 b = 78.24 β = 90 c = 238.47 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2017-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.82 67.5 96.8 20.6 6 38400
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 1JA8 1.82 67.5 36515 1885 96.5 0.193 0.192 0.2011 0.221 0.225 RANDOM 21.94
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] -0.12 -0.06 -0.12 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 15.375 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 5.515 r_long_range_B_refined 4.248 r_long_range_B_other 4.219 r_scangle_other 2.834 r_mcangle_it 2.315 r_mcangle_other 2.315 r_scbond_it 1.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 15.375 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 5.515 r_long_range_B_refined 4.248 r_long_range_B_other 4.219 r_scangle_other 2.834 r_mcangle_it 2.315 r_mcangle_other 2.315 r_scbond_it 1.747 r_scbond_other 1.712 r_mcbond_it 1.392 r_mcbond_other 1.391 r_angle_refined_deg 1.317 r_angle_other_deg 0.908 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3162 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling