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Crystal structure of the ALS-related pathological mutant I113T 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 6.5 289.1 0.1 M MES
20% PEG 3350 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.1K
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.902 α = 90 b = 34.403 β = 112.1 c = 114.999 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 OXFORD ONYX CCD Mirrors 2007-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54056
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 1.9 106.6 98.4 0.112 0.112 6 5.4 44669 44669 12.2
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) 1.9 2 90 0.36 0.36 3.8 2.9 5864
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 1.9 38.95 40616 40616 4053 100 0.24162 0.24162 0.23805 0.2383 0.27687 0.2745 RANDOM 16.854
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] -1.8 -0.87 3.04 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.191 r_dihedral_angle_3_deg 19.225 r_dihedral_angle_4_deg 15.606 r_dihedral_angle_1_deg 8.081 r_scangle_it 4.657 r_scbond_it 3.22 r_angle_refined_deg 2.248 r_mcangle_it 2.108 r_mcbond_it 1.373 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.191 r_dihedral_angle_3_deg 19.225 r_dihedral_angle_4_deg 15.606 r_dihedral_angle_1_deg 8.081 r_scangle_it 4.657 r_scbond_it 3.22 r_angle_refined_deg 2.248 r_mcangle_it 2.108 r_mcbond_it 1.373 r_nbtor_refined 0.311 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.228 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.15 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 4042 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling