☰ Navigation Tabs
Crystal structure of the peroxide-bound manganese superoxide dismutase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D5N PDB entry 1D5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 50 mM Bicine pH 8.5, 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.849 α = 90 b = 107.418 β = 90 c = 180.044 γ = 90
Symmetry Space Group C 2 2 21
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 Mirrors 2000-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 28.3 99.2 0.0822 10.4 154389 139669 2 2 13.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.55 1.61 82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1D5N 1.55 28.3 2 2 154389 118082 6254 88.23 0.22926 0.22711 0.2272 0.26998 0.2307 RANDOM 6.295
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] -0.05 0.83 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.302 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_4_deg 10.799 r_dihedral_angle_1_deg 5.874 r_sphericity_free 4.733 r_scangle_it 2.408 r_sphericity_bonded 2.264 r_scbond_it 1.809 r_angle_refined_deg 1.323 r_mcangle_it 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.302 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_4_deg 10.799 r_dihedral_angle_1_deg 5.874 r_sphericity_free 4.733 r_scangle_it 2.408 r_sphericity_bonded 2.264 r_scbond_it 1.809 r_angle_refined_deg 1.323 r_mcangle_it 1.11 r_rigid_bond_restr 1.106 r_mcbond_it 0.783 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6512 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling