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Mutant of Superoxide Dismutase sodfm2 from Bacteroides fragilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 10 mM zinc chloride, 100 mM sodium acetate pH 5.0 and 20% w/v polyethylene glycol 6000.
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.43 α = 90 b = 117.11 β = 90 c = 139.33 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 EIGER2 XE 16M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89842 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 69 100 0.158 0.17 0.064 0.999 11 13.5 88446
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 2.04 97.6 0.444 1.4 14.2
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 1UES 2 69 88365 4329 99.986 0.194 0.1927 0.1927 0.2289 0.2292 38.986
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] -0.031 -0.86 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.642 r_dihedral_angle_3_deg 15.492 r_lrange_it 7.818 r_lrange_other 7.815 r_scangle_it 6.839 r_scangle_other 6.838 r_dihedral_angle_1_deg 6.248 r_dihedral_angle_2_deg 6.113 r_scbond_it 5.1 r_scbond_other 5.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.642 r_dihedral_angle_3_deg 15.492 r_lrange_it 7.818 r_lrange_other 7.815 r_scangle_it 6.839 r_scangle_other 6.838 r_dihedral_angle_1_deg 6.248 r_dihedral_angle_2_deg 6.113 r_scbond_it 5.1 r_scbond_other 5.099 r_mcangle_it 4.838 r_mcangle_other 4.837 r_mcbond_it 4.046 r_mcbond_other 4.045 r_angle_refined_deg 1.546 r_angle_other_deg 0.532 r_symmetry_nbd_refined 0.283 r_symmetry_xyhbond_nbd_refined 0.273 r_nbd_refined 0.226 r_nbd_other 0.209 r_nbtor_refined 0.193 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.156 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.073 r_ncsr_local_group_6 0.069 r_ncsr_local_group_7 0.067 r_ncsr_local_group_12 0.066 r_ncsr_local_group_11 0.065 r_ncsr_local_group_1 0.064 r_ncsr_local_group_8 0.064 r_ncsr_local_group_9 0.063 r_symmetry_xyhbond_nbd_other 0.062 r_ncsr_local_group_2 0.062 r_metal_ion_refined 0.061 r_ncsr_local_group_14 0.06 r_ncsr_local_group_10 0.059 r_ncsr_local_group_13 0.058 r_ncsr_local_group_5 0.056 r_ncsr_local_group_3 0.055 r_ncsr_local_group_15 0.053 r_ncsr_local_group_4 0.043 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9216 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling pointless data scaling xia2 data reduction MolProbity model building PHASER phasing BUCCANEER model building Coot model building XDS data reduction