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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 PDB ENTRY 1AZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5, 17% PEG 4000, 15% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 289 KK
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.47 α = 90 b = 118.47 β = 90 c = 81.79 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 IMAGE PLATE MAR scanner 345 mm plate 2007-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
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 2.04 23.99 97.8 0.103 11 3.9 41012
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) 2.04 2.15 87 0.47 2.8 3.5 5335
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 2.05 23 38935 2070 99.4 0.20347 0.20113 0.2011 0.24788 0.2477 RANDOM 20.679
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.043 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_4_deg 12.623 r_dihedral_angle_1_deg 5.887 r_scangle_it 1.813 r_angle_refined_deg 1.072 r_scbond_it 1.051 r_mcangle_it 0.802 r_mcbond_it 0.6 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.043 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_4_deg 12.623 r_dihedral_angle_1_deg 5.887 r_scangle_it 1.813 r_angle_refined_deg 1.072 r_scbond_it 1.051 r_mcangle_it 0.802 r_mcbond_it 0.6 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.07 r_metal_ion_refined 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 4448 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling