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Structure of the superoxide dismutase (Fe) (sodB) from Coxiella burnetii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ISA PDB CODE 1ISA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 M imidazole, 10% PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.102 α = 90 b = 65.285 β = 90 c = 110.069 γ = 90
Symmetry Space Group P 21 21 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 CCD RIGAKU SATURN 944 2011-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2 100 93.2 0.066 34.2 13.5 29777 27752 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 71.1 0.251 4.1 3.6 1456
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 (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 CODE 1ISA 2.004 56.15 29791 27134 1388 91.08 0.23494 0.23301 0.2457 0.27066 0.2821 RANDOM 25.616
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] -0.94 -0.8 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.057 r_dihedral_angle_3_deg 12.338 r_dihedral_angle_4_deg 9.019 r_dihedral_angle_1_deg 5.18 r_scangle_it 0.974 r_angle_refined_deg 0.879 r_angle_other_deg 0.786 r_scbond_it 0.602 r_mcangle_it 0.359 r_mcbond_it 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.057 r_dihedral_angle_3_deg 12.338 r_dihedral_angle_4_deg 9.019 r_dihedral_angle_1_deg 5.18 r_scangle_it 0.974 r_angle_refined_deg 0.879 r_angle_other_deg 0.786 r_scbond_it 0.602 r_mcangle_it 0.359 r_mcbond_it 0.186 r_chiral_restr 0.055 r_mcbond_other 0.035 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3134 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling