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A4V mutant of human SOD1 bound with N-aryl benzoisoselenazolone derivative 13 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 2.04 39.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.07 α = 90 b = 68.09 β = 106.87 c = 50.86 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 PILATUS3 6M mirrors 2020-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.25 39.6 92.3 0.078 0.106 0.072 0.999 8 3.2 69892 7.912
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 1.25 1.27 99.3 0.562 0.756 0.501 0.524 2.2 3.2
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 1UXM 1.25 39.6 69865 3480 99.281 0.178 0.1776 0.1874 0.1912 0.1997 13.096
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] 0.224 0.196 -0.412 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_other_3_deg 21.389 r_dihedral_angle_4_deg 14.327 r_dihedral_angle_3_deg 11.76 r_dihedral_angle_1_deg 7.079 r_lrange_it 4.442 r_lrange_other 4.287 r_scangle_it 3.961 r_scangle_other 3.922 r_scbond_it 2.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_other_3_deg 21.389 r_dihedral_angle_4_deg 14.327 r_dihedral_angle_3_deg 11.76 r_dihedral_angle_1_deg 7.079 r_lrange_it 4.442 r_lrange_other 4.287 r_scangle_it 3.961 r_scangle_other 3.922 r_scbond_it 2.695 r_scbond_other 2.645 r_angle_refined_deg 1.901 r_mcangle_other 1.858 r_mcangle_it 1.856 r_angle_other_deg 1.571 r_mcbond_it 1.221 r_mcbond_other 1.221 r_symmetry_nbd_refined 0.293 r_nbd_refined 0.26 r_nbd_other 0.242 r_metal_ion_refined 0.209 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.127 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2220 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing