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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 293.15 200 mM sodium chloride, 100 mM Tris pH 8.5 and 25 % w/v polyethylene glycol 3350.
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.13 α = 90 b = 100.11 β = 91.8 c = 103.6 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 PIXEL DECTRIS EIGER2 X 16M 2021-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89843 Diamond I03
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 1.6 103.55 100 0.998 12 7 190799
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 1.6 1.63 0.548 7.2
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 1.6 103.549 190767 9665 99.988 0.137 0.1333 0.1333 0.2038 0.2038 22.889
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] 0.039 0.17 -0.099 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.922 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_2_deg 6.945 r_scangle_it 6.874 r_scangle_other 6.873 r_scbond_it 6.435 r_scbond_other 6.435 r_lrange_it 6.397 r_lrange_other 6.285 r_dihedral_angle_1_deg 6.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.922 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_2_deg 6.945 r_scangle_it 6.874 r_scangle_other 6.873 r_scbond_it 6.435 r_scbond_other 6.435 r_lrange_it 6.397 r_lrange_other 6.285 r_dihedral_angle_1_deg 6.15 r_rigid_bond_restr 5.618 r_mcangle_it 5 r_mcangle_other 5 r_mcbond_it 4.401 r_mcbond_other 4.401 r_angle_refined_deg 1.485 r_angle_other_deg 0.548 r_symmetry_xyhbond_nbd_refined 0.213 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.203 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.181 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_8 0.087 r_ncsr_local_group_10 0.086 r_ncsr_local_group_17 0.086 r_chiral_restr 0.085 r_ncsr_local_group_6 0.083 r_ncsr_local_group_11 0.083 r_ncsr_local_group_9 0.082 r_ncsr_local_group_13 0.082 r_ncsr_local_group_26 0.082 r_ncsr_local_group_1 0.081 r_ncsr_local_group_21 0.079 r_ncsr_local_group_23 0.079 r_ncsr_local_group_12 0.078 r_ncsr_local_group_14 0.077 r_ncsr_local_group_28 0.077 r_ncsr_local_group_16 0.076 r_ncsr_local_group_24 0.076 r_ncsr_local_group_2 0.075 r_ncsr_local_group_22 0.075 r_ncsr_local_group_4 0.074 r_ncsr_local_group_3 0.073 r_ncsr_local_group_18 0.072 r_ncsr_local_group_25 0.072 r_symmetry_nbtor_other 0.071 r_ncsr_local_group_19 0.068 r_ncsr_local_group_5 0.067 r_ncsr_local_group_20 0.066 r_ncsr_local_group_15 0.065 r_ncsr_local_group_27 0.063 r_ncsr_local_group_7 0.058 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 12304 Nucleic Acid Atoms Solvent Atoms 1507 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing Coot model building