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Human SOD1 in complex with S-XL6 cross-linker
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 293 2.5M ammonium sulphate, 150mM NaCl, sodium acetate pH 4.75
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.81 α = 90 b = 68.02 β = 105.85 c = 50.69 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 EIGER R 4M 2023-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ 1.54180
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 1.665 37.362 95.2 0.145 0.197 0.133 0.97 83.8 3.4 28274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.69 0.417 0.578 0.399 0.757 3.5
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 2C9V 1.665 37.362 28270 1400 95.073 0.186 0.1841 0.1827 0.2327 0.2302 19.318
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] 0.054 0.233 -0.359 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.771 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_3_deg 12.955 r_dihedral_angle_other_3_deg 12.544 r_dihedral_angle_1_deg 7.688 r_lrange_it 5.056 r_lrange_other 4.86 r_scangle_it 3.293 r_scangle_other 3.292 r_mcangle_it 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.771 r_dihedral_angle_4_deg 13.865 r_dihedral_angle_3_deg 12.955 r_dihedral_angle_other_3_deg 12.544 r_dihedral_angle_1_deg 7.688 r_lrange_it 5.056 r_lrange_other 4.86 r_scangle_it 3.293 r_scangle_other 3.292 r_mcangle_it 2.412 r_mcangle_other 2.411 r_scbond_it 2.184 r_scbond_other 2.183 r_mcbond_it 1.66 r_mcbond_other 1.66 r_angle_refined_deg 1.605 r_angle_other_deg 1.439 r_symmetry_nbd_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.284 r_nbd_other 0.234 r_nbd_refined 0.226 r_symmetry_nbd_other 0.195 r_metal_ion_refined 0.172 r_xyhbond_nbd_refined 0.163 r_nbtor_refined 0.152 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_bond_other_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2220 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOSFLM data reduction REFMAC phasing