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X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2APS PDB ENTRY 2APS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 PEG 8000, sodium cacodylate, sodium acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 1.98 37.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.32 α = 66.59 b = 65.9 β = 89.87 c = 69.54 γ = 76.03
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 2001-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9340 ESRF ID14-1
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 19.5 93.8 0.064 0.064 10.83 3.1 88269 88269 20.284
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 88.6 0.278 0.278 4.53 2.99 13302
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 2APS 1.5 19.5 85257 85257 4488 100 0.15834 0.15834 0.15651 0.164 0.19332 0.1991 RANDOM 14.838
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] -0.04 -0.38 -0.16 0.23 -0.28 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 32.247 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 6.247 r_scangle_it 4.33 r_scbond_it 3.393 r_mcangle_it 2.168 r_mcbond_it 1.816 r_angle_refined_deg 1.514 r_angle_other_deg 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.865 r_dihedral_angle_4_deg 32.247 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 6.247 r_scangle_it 4.33 r_scbond_it 3.393 r_mcangle_it 2.168 r_mcbond_it 1.816 r_angle_refined_deg 1.514 r_angle_other_deg 0.801 r_symmetry_hbond_refined 0.277 r_mcbond_other 0.277 r_nbd_refined 0.201 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.176 r_symmetry_vdw_other 0.139 r_symmetry_vdw_refined 0.116 r_chiral_restr 0.091 r_nbtor_other 0.084 r_bond_refined_d 0.014 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 r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4644 Nucleic Acid Atoms Solvent Atoms 1082 Heterogen Atoms 94
Software Software Software Name Purpose XDS data reduction AMoRE phasing REFMAC refinement XDS data scaling