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X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other as-isolated native model obtained for the same protein by the MAD method
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 = 225.68 α = 90 b = 225.68 β = 90 c = 225.68 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 ADSC QUANTUM 4 toroidal mirrors 2000-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 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 2.05 30 99 0.057 8.1 3.7 234647 234647 29
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 2.05 2.12 99.8 0.299 2.4 3.6 23163
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 structure solved using the native as-isolated structure as starting model THROUGHOUT as-isolated native model obtained for the same protein by the MAD method 2.05 30 229756 229756 4891 99 0.231 0.231 0.1958 0.27 0.2421 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 23787.42
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.077 s_non_zero_chiral_vol 0.028 s_angle_d 0.018 s_from_restr_planes 0.0179 s_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21168 Nucleic Acid Atoms Solvent Atoms 1659 Heterogen Atoms 704
Software Software Software Name Purpose SHELXL-97 refinement SCALA data scaling CNS refinement DENZO data reduction CCP4 data scaling CNS phasing