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Human SOD1 low dose data collecton
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.75 293 2.5 M Ammonium sulphate, Acetate buffer pH 4.75
Crystal Properties Matthews coefficient Solvent content 2.11 0.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.26 α = 90 b = 68.01 β = 106.28 c = 52.58 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 EIGER R 4M 2023-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54180
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 1.77 37.69 97.3 0.135 0.184 0.125 0.974 3.9 3.3 25235
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 1.77 1.81 0.411 0.569 0.393 0.649 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.77 35.338 25220 933 97.221 0.211 0.2089 0.2505 0.2793 19.766
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] 0.994 -1.423 -1.241 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.885 r_dihedral_angle_3_deg 14.812 r_dihedral_angle_4_deg 14.336 r_dihedral_angle_1_deg 9.904 r_lrange_it 5.173 r_lrange_other 4.815 r_scangle_it 3.067 r_scangle_other 3.031 r_mcangle_it 2.4 r_mcangle_other 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.885 r_dihedral_angle_3_deg 14.812 r_dihedral_angle_4_deg 14.336 r_dihedral_angle_1_deg 9.904 r_lrange_it 5.173 r_lrange_other 4.815 r_scangle_it 3.067 r_scangle_other 3.031 r_mcangle_it 2.4 r_mcangle_other 2.4 r_scbond_it 1.923 r_scbond_other 1.886 r_angle_refined_deg 1.659 r_mcbond_it 1.522 r_mcbond_other 1.518 r_angle_other_deg 1.272 r_symmetry_nbd_refined 0.259 r_symmetry_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_refined 0.191 r_nbd_refined 0.181 r_symmetry_nbd_other 0.176 r_nbd_other 0.168 r_nbtor_refined 0.134 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.073 r_metal_ion_refined 0.038 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2220 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement REFMAC refinement MAR345dtb data collection MOSFLM data reduction Aimless data scaling MOLREP phasing