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Crystal structure of iron superoxide dismutase from Anaplasma phagocytophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UNF PDB entry 1UNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 PACT screen condition E1, 20% PEG 3350, 0.2 M NaF. 0.4/0.4 microliter drops. 30.0 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% Glycerol, 2 mM DTT. Crystal tracking ID 204869e1, expression tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.66 α = 102.09 b = 66.6 β = 104.83 c = 85.44 γ = 88.58
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+ 2009-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.95 40 91.1 0.036 14.37 116074 63217 -3 25.647
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 1.95 2 83.1 0.203 2.6 4284
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 1UNF 1.95 40 63217 3182 91.17 0.169 0.167 0.178 0.206 0.2175 RANDOM 12.299
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] -1.17 -0.02 -0.13 1.02 0.45 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.295 r_dihedral_angle_4_deg 19.704 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_1_deg 5.447 r_scangle_it 2.853 r_scbond_it 1.784 r_angle_refined_deg 1.222 r_mcangle_it 1.017 r_mcbond_it 0.552 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.295 r_dihedral_angle_4_deg 19.704 r_dihedral_angle_3_deg 14.071 r_dihedral_angle_1_deg 5.447 r_scangle_it 2.853 r_scbond_it 1.784 r_angle_refined_deg 1.222 r_mcangle_it 1.017 r_mcbond_it 0.552 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6509 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 8
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction