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A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 5 in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 292 100mM NaOAc pH 4.7, 150mM NaCl, 2.5M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.495 α = 90 b = 68.321 β = 106.362 c = 51.321 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 XE 16M mirrors 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.55 36.964 99.8 0.042 0.058 0.04 0.998 11.6 3.2 36977 17.407
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 1.55 1.58 99.6 0.279 0.376 0.25 0.887 2 3.3
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 1UXM 1.55 36.964 36948 1835 99.779 0.19 0.1891 0.1969 0.2077 0.2151 21.058
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] 1.165 -0.19 -0.987 -0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.215 r_dihedral_angle_other_3_deg 35.286 r_dihedral_angle_4_deg 23.587 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 7.22 r_lrange_it 5.749 r_lrange_other 5.71 r_scangle_it 4.735 r_scangle_other 4.733 r_scbond_it 3.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.215 r_dihedral_angle_other_3_deg 35.286 r_dihedral_angle_4_deg 23.587 r_dihedral_angle_3_deg 14.367 r_dihedral_angle_1_deg 7.22 r_lrange_it 5.749 r_lrange_other 5.71 r_scangle_it 4.735 r_scangle_other 4.733 r_scbond_it 3.222 r_scbond_other 3.221 r_mcangle_it 2.833 r_mcangle_other 2.832 r_mcbond_it 2 r_mcbond_other 2 r_angle_refined_deg 1.746 r_angle_other_deg 1.577 r_symmetry_nbd_refined 0.352 r_nbd_other 0.282 r_nbd_refined 0.256 r_symmetry_nbd_other 0.197 r_metal_ion_refined 0.192 r_xyhbond_nbd_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.16 r_ncsr_local_group_1 0.09 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2201 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing