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Crystal structure of the ALS-related pathological mutant T54R of human apo Cu,Zn Superoxide Dismutase (SOD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289.1 0.1 M HEPES
20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.1K
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.94 α = 90 b = 34.033 β = 112.14 c = 114.585 γ = 90
Symmetry Space Group C 1 2 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 CCD MAR CCD 165 mm Si 111 2007-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.99180 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 39.2 96 0.098 0.098 6.4 3.3 29951 29951 29.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.3 91.2 0.443 0.443 1.9 2.6 4106
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1HL5 2.15 39.19 27233 27233 2715 100 0.20907 0.20907 0.2003 0.1995 0.2972 0.2906 RANDOM 26.25
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] -1.69 -2.58 2.28 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.603 r_dihedral_angle_3_deg 19.858 r_dihedral_angle_4_deg 16.616 r_dihedral_angle_1_deg 8.506 r_scangle_it 4.896 r_scbond_it 3.372 r_angle_refined_deg 2.248 r_mcangle_it 2.128 r_mcbond_it 1.306 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.603 r_dihedral_angle_3_deg 19.858 r_dihedral_angle_4_deg 16.616 r_dihedral_angle_1_deg 8.506 r_scangle_it 4.896 r_scbond_it 3.372 r_angle_refined_deg 2.248 r_mcangle_it 2.128 r_mcbond_it 1.306 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.272 r_xyhbond_nbd_refined 0.228 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.203 r_chiral_restr 0.158 r_bond_refined_d 0.025 r_gen_planes_refined 0.009 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_refined 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 4028 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling