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A Bacteroidetes bacterium CuZn-superoxide dismutase with CuZn metalation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 .12 M alcohol mix containing 1,6-hexanediol, 1-butanol 1,2-propanediol, 2-propanol, 4-butanediol, 1,3-propanediol; 0.1 M buffer mix containing sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 3-(N-morpholino)propane sulfonic acid pH 7.5; 37.5 % precipitant mix containing 2-Methyl-2,4-pentanediol, polyethylene glycol 1000, polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.79 α = 90 b = 109.593 β = 90 c = 122.598 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.7 81.71 100 0.999 10.6 9.2 16195
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 0.61
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7B4O 2.7 81.7 16146 803 99.963 0.242 0.2396 0.2514 0.2783 0.2869 89.467
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] 0.931 2.595 -3.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.359 r_dihedral_angle_3_deg 12.751 r_dihedral_angle_4_deg 6.934 r_dihedral_angle_1_deg 5.934 r_lrange_it 3.668 r_lrange_other 3.667 r_angle_refined_deg 1.213 r_angle_other_deg 1.067 r_mcangle_it 0.81 r_mcangle_other 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.359 r_dihedral_angle_3_deg 12.751 r_dihedral_angle_4_deg 6.934 r_dihedral_angle_1_deg 5.934 r_lrange_it 3.668 r_lrange_other 3.667 r_angle_refined_deg 1.213 r_angle_other_deg 1.067 r_mcangle_it 0.81 r_mcangle_other 0.81 r_scangle_it 0.56 r_scangle_other 0.56 r_mcbond_it 0.45 r_mcbond_other 0.45 r_scbond_it 0.299 r_scbond_other 0.299 r_symmetry_nbd_refined 0.184 r_nbd_other 0.176 r_nbd_refined 0.154 r_symmetry_nbd_other 0.151 r_nbtor_refined 0.133 r_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.064 r_ncsr_local_group_5 0.064 r_ncsr_local_group_6 0.064 r_ncsr_local_group_1 0.062 r_ncsr_local_group_3 0.062 r_ncsr_local_group_4 0.061 r_ncsr_local_group_2 0.045 r_metal_ion_refined 0.038 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4427 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing