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Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AZV PDB entry 1AZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 297 20% polyethylene glycol 1000, imidazole pH 8.0, calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 4.12 70.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.576 α = 90 b = 194.331 β = 90 c = 143.179 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII mirrors 2007-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.2 50 99.8 0.088 14.7 4.5 79657 35.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 100 0.503 2.9 4.4 7908
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1AZV 2.2 28.07 75634 3992 99.79 0.20699 0.20512 0.2033 0.24229 0.2412 RANDOM 31.667
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] -0.15 -0.05 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.632 r_dihedral_angle_3_deg 16.127 r_dihedral_angle_4_deg 12.502 r_dihedral_angle_1_deg 6.121 r_scangle_it 3.415 r_scbond_it 2.06 r_mcangle_it 1.441 r_angle_refined_deg 1.293 r_mcbond_it 0.762 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.632 r_dihedral_angle_3_deg 16.127 r_dihedral_angle_4_deg 12.502 r_dihedral_angle_1_deg 6.121 r_scangle_it 3.415 r_scbond_it 2.06 r_mcangle_it 1.441 r_angle_refined_deg 1.293 r_mcbond_it 0.762 r_nbtor_refined 0.296 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.101 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6660 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 11
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling