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A4V 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 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 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.95 α = 90 b = 67.72 β = 106.4 c = 50.65 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 mirrors 2020-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 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 1.45 39.51 99.3 0.046 0.063 0.043 0.998 10.6 3.3 44399 16.111
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 99.8 0.585 0.787 0.523 0.686 1.8 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 1.45 39.51 44377 2259 99.211 0.158 0.1556 0.1655 0.1933 0.1992 21.212
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] 0.876 0.29 -1.496 0.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 51.638 r_dihedral_angle_2_deg 36.722 r_dihedral_angle_3_deg 12.314 r_dihedral_angle_4_deg 10.52 r_dihedral_angle_1_deg 7.346 r_rigid_bond_restr 4.59 r_scangle_it 3.957 r_scbond_it 3.761 r_scbond_other 3.481 r_scangle_other 3.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 51.638 r_dihedral_angle_2_deg 36.722 r_dihedral_angle_3_deg 12.314 r_dihedral_angle_4_deg 10.52 r_dihedral_angle_1_deg 7.346 r_rigid_bond_restr 4.59 r_scangle_it 3.957 r_scbond_it 3.761 r_scbond_other 3.481 r_scangle_other 3.291 r_lrange_it 3.004 r_lrange_other 2.937 r_mcangle_it 2.212 r_mcangle_other 2.212 r_angle_refined_deg 2.205 r_mcbond_it 2.13 r_mcbond_other 2.13 r_angle_other_deg 1.663 r_symmetry_nbd_refined 0.377 r_nbd_other 0.286 r_symmetry_xyhbond_nbd_refined 0.285 r_nbd_refined 0.241 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.13 r_ncsr_local_group_1 0.118 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.039 r_gen_planes_refined 0.012 r_gen_planes_other 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2210 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing