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A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 2 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, 2.6M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.613 α = 90 b = 68.289 β = 105.759 c = 50.899 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 PILATUS 6M-F 2020-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
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 1.95 39.84 99.7 0.065 0.091 0.063 0.985 7.4 3.1 18560 26.659
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 1.95 2 98.9 0.344 0.48 0.333 0.538 2.3 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1UXM 1.95 39.836 18533 871 99.586 0.222 0.221 0.242 0.2655 29.501
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] 2.127 0.057 -1.631 -0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 57.119 r_dihedral_angle_2_deg 37.962 r_dihedral_angle_4_deg 19.931 r_dihedral_angle_3_deg 12.251 r_lrange_it 7.712 r_lrange_other 7.67 r_dihedral_angle_1_deg 7.657 r_scangle_it 5.514 r_scangle_other 5.381 r_scbond_it 3.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 57.119 r_dihedral_angle_2_deg 37.962 r_dihedral_angle_4_deg 19.931 r_dihedral_angle_3_deg 12.251 r_lrange_it 7.712 r_lrange_other 7.67 r_dihedral_angle_1_deg 7.657 r_scangle_it 5.514 r_scangle_other 5.381 r_scbond_it 3.92 r_scbond_other 3.78 r_mcangle_it 3.678 r_mcangle_other 3.676 r_mcbond_it 2.671 r_mcbond_other 2.67 r_angle_refined_deg 1.608 r_angle_other_deg 1.578 r_nbd_other 0.336 r_symmetry_nbd_refined 0.307 r_metal_ion_refined 0.256 r_nbd_refined 0.217 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.103 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2197 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing