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X-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other polyalanine model, built from scratch
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.3 α = 90 b = 225.3 β = 90 c = 225.3 γ = 90
Symmetry Space Group P 21 3
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 MARRESEARCH collimating and focusing mirrors 1999-09-15 M MAD 2 1 x-ray 100 CCD ADSC QUANTUM 4 toroidal mirrors 2000-02-02 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.992, 1.7387, 1.74 ESRF BM14 2 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1,2 1.95 30 98.9 0.066 6.4 3.3 271259 271259 28
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) 1,2 1.95 2.02 97.6 0.343 2.1 3.1
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 MAD THROUGHOUT polyalanine model, built from scratch 1.95 30 265820 265820 5260 98.9 0.214 0.214 0.1851 0.254 0.2336 thin resolution shells 31.6
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 24247.95
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.071 s_non_zero_chiral_vol 0.031 s_angle_d 0.025 s_zero_chiral_vol 0.025 s_from_restr_planes 0.019 s_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21300 Nucleic Acid Atoms Solvent Atoms 1890 Heterogen Atoms 829
Software Software Software Name Purpose DENZO data reduction SCALA data scaling SnB phasing MLPHARE phasing DM model building SHELXL-97 refinement CCP4 data scaling DM phasing