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A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 3 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 2.01 38.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.334 α = 90 b = 68.26 β = 105.711 c = 50.706 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 2019-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8500 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 32.483 100 0.071 0.098 0.068 6.9 3.4 33208 21.834
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 1.6 1.63 99.8 0.398 0.541 0.364 0.774 2 3.4
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 1.6 32.46 33183 1632 99.937 0.187 0.1858 0.1911 0.2171 0.2228 23.867
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] 0.86 -0.692 -0.55 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.385 r_dihedral_angle_other_3_deg 26.966 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_4_deg 13.473 r_dihedral_angle_1_deg 13.003 r_lrange_it 5.295 r_lrange_other 5.295 r_scangle_it 4.052 r_scangle_other 4.051 r_mcangle_it 3.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.385 r_dihedral_angle_other_3_deg 26.966 r_dihedral_angle_3_deg 14.978 r_dihedral_angle_4_deg 13.473 r_dihedral_angle_1_deg 13.003 r_lrange_it 5.295 r_lrange_other 5.295 r_scangle_it 4.052 r_scangle_other 4.051 r_mcangle_it 3.198 r_mcangle_other 3.198 r_scbond_it 2.727 r_scbond_other 2.726 r_mcbond_it 2.324 r_mcbond_other 2.299 r_angle_refined_deg 1.643 r_angle_other_deg 1.466 r_symmetry_nbd_refined 0.401 r_nbd_refined 0.289 r_nbd_other 0.22 r_metal_ion_refined 0.201 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.162 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.121 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2222 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing