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Superoxide dismutase from Aeropyrum pernix K1, Fe-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AK1 PDB ENTRY 3AK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM HEPES, 10% PEG 6000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 36.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.057 α = 90 b = 71.755 β = 91.72 c = 76.404 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE 2010-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.48 50 95.9 0.077 16.6 124631 119558 18.324
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) 1.48 1.53 88.9 0.383 3.6 5.2 11055
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3AK1 1.48 49.75 113539 5993 96.33 0.22692 0.22536 0.2247 0.25621 0.2559 RANDOM 21.463
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.24 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_1_deg 6.114 r_scangle_it 2.103 r_scbond_it 1.444 r_angle_refined_deg 1.143 r_mcangle_it 0.873 r_mcbond_it 0.694 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.24 r_dihedral_angle_4_deg 15.7 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_1_deg 6.114 r_scangle_it 2.103 r_scbond_it 1.444 r_angle_refined_deg 1.143 r_mcangle_it 0.873 r_mcbond_it 0.694 r_nbtor_refined 0.309 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.079 r_metal_ion_refined 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 6855 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 44
Software Software Software Name Purpose BSS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing