☰ Navigation Tabs
Superoxide dismutase SodFM1 from CPR Parkubacteria Wolfebacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 100 mM sodium acetate trihydrate pH 4.5 and 25% w/v polyethylene glycol 3350.
Crystal Properties Matthews coefficient Solvent content 1.99 38.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.531 α = 90 b = 70.586 β = 100.301 c = 57.788 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 2.1 70.59 100 0.996 7.3 14.1 21632
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 2.1 2.16 0.64 1
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 1IX9 2.1 56.857 21594 1048 99.907 0.211 0.2089 0.209 0.2563 0.2563 37.345
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] -1.993 1.639 2.519 -1.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.401 r_dihedral_angle_6_deg 15.353 r_dihedral_angle_1_deg 6.541 r_lrange_other 5.666 r_lrange_it 5.664 r_scangle_it 4.805 r_scangle_other 4.804 r_dihedral_angle_2_deg 4.656 r_mcangle_it 3.595 r_mcangle_other 3.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.401 r_dihedral_angle_6_deg 15.353 r_dihedral_angle_1_deg 6.541 r_lrange_other 5.666 r_lrange_it 5.664 r_scangle_it 4.805 r_scangle_other 4.804 r_dihedral_angle_2_deg 4.656 r_mcangle_it 3.595 r_mcangle_other 3.595 r_scbond_it 3.41 r_scbond_other 3.409 r_mcbond_it 2.631 r_mcbond_other 2.62 r_angle_refined_deg 1.827 r_angle_other_deg 0.625 r_nbd_other 0.247 r_nbd_refined 0.243 r_symmetry_nbd_refined 0.234 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.196 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_1 0.098 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.076 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_metal_ion_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing BUCCANEER model building Coot model building