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A4V mutant of human SOD1 bound with 2-(pyridin-3-ylmethyl)benzoisoselenazolone derivative 9 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, 2.7M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.02 39.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.93 α = 90 b = 67.49 β = 106.12 c = 50.78 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 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 1.5 34.69 95.2 0.058 0.079 0.054 0.994 9.7 3.5 38401 13.797
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 1.5 1.53 82 0.465 0.631 0.424 0.745 1.9 3.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1UXM 1.6 34.69 32156 1614 96.353 0.183 0.1819 0.2081 0.2025 20.626
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] 1.531 0.522 -1.918 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.127 r_dihedral_angle_4_deg 23.29 r_dihedral_angle_3_deg 12.503 r_dihedral_angle_1_deg 7.238 r_lrange_it 5.159 r_scangle_it 4.799 r_scbond_it 3.275 r_mcangle_it 2.441 r_angle_refined_deg 1.754 r_mcbond_it 1.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.127 r_dihedral_angle_4_deg 23.29 r_dihedral_angle_3_deg 12.503 r_dihedral_angle_1_deg 7.238 r_lrange_it 5.159 r_scangle_it 4.799 r_scbond_it 3.275 r_mcangle_it 2.441 r_angle_refined_deg 1.754 r_mcbond_it 1.723 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.265 r_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.23 r_ncsr_local_group_1 0.13 r_metal_ion_refined 0.126 r_chiral_restr 0.125 r_xyhbond_nbd_refined 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2221 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing