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Superoxide dismutase from Aeropyrum pernix K1, apo-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WB8 PDB ENTRY 1WB8
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 1.95 36.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.26 α = 90 b = 72.251 β = 90.99 c = 76.652 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 IMAGE PLATE MAC Science DIP-2040 2009-10-15 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 1.56 50 98 0.073 23 4.4 106085 103949 19.75
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) 1.56 1.62 92.4 0.396 2.9 2.7 9723
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WB8 1.57 36.13 98731 5190 97.83 0.19835 0.1964 0.1965 0.23638 0.2363 RANDOM 25.897
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 36.567 r_dihedral_angle_4_deg 18.342 r_dihedral_angle_3_deg 13.093 r_dihedral_angle_1_deg 5.738 r_scangle_it 2.246 r_scbond_it 1.487 r_angle_refined_deg 1.136 r_mcangle_it 0.844 r_mcbond_it 0.814 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.567 r_dihedral_angle_4_deg 18.342 r_dihedral_angle_3_deg 13.093 r_dihedral_angle_1_deg 5.738 r_scangle_it 2.246 r_scbond_it 1.487 r_angle_refined_deg 1.136 r_mcangle_it 0.844 r_mcbond_it 0.814 r_nbtor_refined 0.305 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.1 r_chiral_restr 0.084 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_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 6910 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 104
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling