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G93A mutant of human SOD1 bound with Ebselen in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WKO
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 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.672 α = 90 b = 67.989 β = 105.61 c = 50.422 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 X 9M 2021-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.980000 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 1.4 67.99 99.4 0.109 0.151 0.104 0.976 5.4 3 49165
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 1.4 1.42 93.5 0.496 0.619 0.468 0.576 1.6 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 2WKO 1.4 48.609 49165 2551 99.377 0.204 0.2029 0.2065 0.2249 0.2295 14.357
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] 1.144 -0.432 -1.079 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_other_3_deg 29.792 r_dihedral_angle_4_deg 23.177 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 7.316 r_lrange_it 4.127 r_lrange_other 3.981 r_scangle_it 2.749 r_scangle_other 2.748 r_scbond_it 1.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_other_3_deg 29.792 r_dihedral_angle_4_deg 23.177 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 7.316 r_lrange_it 4.127 r_lrange_other 3.981 r_scangle_it 2.749 r_scangle_other 2.748 r_scbond_it 1.803 r_scbond_other 1.802 r_mcangle_it 1.719 r_mcangle_other 1.716 r_angle_refined_deg 1.69 r_angle_other_deg 1.561 r_mcbond_it 1.049 r_mcbond_other 1.049 r_metal_ion_refined 0.394 r_nbd_other 0.213 r_nbd_refined 0.191 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.157 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.08 r_chiral_restr 0.065 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2193 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing