☰ Navigation Tabs
X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z9N PDB entry 1Z9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 sodium cytrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.26 45.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.41 α = 90 b = 63.99 β = 118.04 c = 73.97 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 MARRESEARCH mirrors 2001-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R
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 1.5 20 97.4 0.05 0.05 17.99 3.93 46454 23.455
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 1.5 1.59 91.4 0.178 0.178 6.62 3.31 6883
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 PDB entry 1Z9N 1.5 19.32 44131 44131 2323 100 0.17228 0.17228 0.17021 0.1713 0.21238 0.2137 RANDOM 16.471
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] -0.08 0.28 0.69 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 35.064 r_dihedral_angle_3_deg 12.649 r_sphericity_bonded 7.328 r_dihedral_angle_1_deg 6.332 r_scangle_it 4.098 r_scbond_it 3.066 r_mcangle_it 2.192 r_mcbond_it 1.87 r_angle_refined_deg 1.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 35.064 r_dihedral_angle_3_deg 12.649 r_sphericity_bonded 7.328 r_dihedral_angle_1_deg 6.332 r_scangle_it 4.098 r_scbond_it 3.066 r_mcangle_it 2.192 r_mcbond_it 1.87 r_angle_refined_deg 1.539 r_angle_other_deg 0.832 r_symmetry_hbond_refined 0.349 r_mcbond_other 0.301 r_symmetry_vdw_refined 0.242 r_symmetry_vdw_other 0.208 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.198 r_nbd_other 0.189 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data scaling MOLREP phasing