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A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 6 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 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.24 α = 90 b = 68.32 β = 106.17 c = 50.98 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 1.45 34.33 99.4 0.031 0.042 0.029 0.999 13.3 3.3 44385 16.64
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 1.45 1.47 99.4 0.561 0.769 0.524 0.609 1.4 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 1.45 34.33 44362 2240 99.359 0.195 0.1947 0.2033 0.2092 0.2103 20.308
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] 1.43 -0.209 -0.963 -0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_other_3_deg 32.139 r_dihedral_angle_4_deg 19.259 r_dihedral_angle_3_deg 13.311 r_dihedral_angle_1_deg 7.204 r_lrange_it 5.288 r_lrange_other 5.192 r_scangle_it 4.482 r_scangle_other 4.476 r_scbond_it 3.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_other_3_deg 32.139 r_dihedral_angle_4_deg 19.259 r_dihedral_angle_3_deg 13.311 r_dihedral_angle_1_deg 7.204 r_lrange_it 5.288 r_lrange_other 5.192 r_scangle_it 4.482 r_scangle_other 4.476 r_scbond_it 3.029 r_scbond_other 3.01 r_mcangle_it 2.664 r_mcangle_other 2.664 r_mcbond_it 1.913 r_mcbond_other 1.912 r_angle_refined_deg 1.747 r_angle_other_deg 1.644 r_symmetry_nbd_refined 0.341 r_nbd_refined 0.27 r_symmetry_xyhbond_nbd_refined 0.264 r_nbd_other 0.237 r_metal_ion_refined 0.228 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.124 r_ncsr_local_group_1 0.1 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2196 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing