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Crystal structures of holo and Cu-deficient Cu/ZnSOD from the silkworm Bombyx mori and the implications in Amyotrophic lateral sclerosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 2.0M (NH4)2SO4, 0.1M Tris-HCl, pH 8.5, 10% glycerol, 1mM CuCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.493 α = 90 b = 111.493 β = 90 c = 39.886 γ = 120
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 RAYONIX MX225HE 2009-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9794 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 40 99.4 0.07 21.3 6.2 26262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 99 0.297 5.2 6.2 2560
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 1AZV 1.8 30 24910 1334 99.25 0.22491 0.22311 0.214 0.25759 0.2454 RANDOM 28.479
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] 0.9 0.45 0.9 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.949 r_dihedral_angle_4_deg 14.429 r_dihedral_angle_3_deg 13.268 r_dihedral_angle_1_deg 5.631 r_scangle_it 2.658 r_scbond_it 1.582 r_mcangle_it 1.174 r_angle_refined_deg 1.004 r_mcbond_it 0.64 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.949 r_dihedral_angle_4_deg 14.429 r_dihedral_angle_3_deg 13.268 r_dihedral_angle_1_deg 5.631 r_scangle_it 2.658 r_scbond_it 1.582 r_mcangle_it 1.174 r_angle_refined_deg 1.004 r_mcbond_it 0.64 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2210 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 4
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling