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Superoxide dismutase from Aeropyrum pernix K1, Mn-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, 8% PEG 6000, 8% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.064 α = 90 b = 71.782 β = 91.81 c = 76.853 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 MX-225 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 1.35 50 98 0.048 15.9 7.3 164370 161154 13.812
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) 1.35 1.4 97 0.361 5.8 6.9
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 1.35 31.86 152991 8101 97.81 0.1879 0.1871 0.1863 0.20281 0.2028 RANDOM 16.117
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 35.79 r_dihedral_angle_4_deg 14.129 r_dihedral_angle_3_deg 10.768 r_dihedral_angle_1_deg 5.927 r_scangle_it 1.778 r_scbond_it 1.144 r_angle_refined_deg 1.052 r_mcangle_it 0.672 r_mcbond_it 0.598 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_4_deg 14.129 r_dihedral_angle_3_deg 10.768 r_dihedral_angle_1_deg 5.927 r_scangle_it 1.778 r_scbond_it 1.144 r_angle_refined_deg 1.052 r_mcangle_it 0.672 r_mcbond_it 0.598 r_nbtor_refined 0.306 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.1 r_chiral_restr 0.078 r_bond_refined_d 0.006 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_refined 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 6823 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 76
Software Software Software Name Purpose BSS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing