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Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (iron bound, F16L mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 21% MPD, 0.4M MgCl2, 0.1M Ac pH 4.6, BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: Liu-S-066, well G9, 2. Puck: PSL-1801, Cryo: 35% MPD + crystallant. 5 minute soak in 25 mM ferrous ammonium sulfate in cryo
Crystal Properties Matthews coefficient Solvent content 3.19 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.032 α = 90 b = 113.032 β = 90 c = 113.032 γ = 90
Symmetry Space Group P 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2022-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.65 46.15 100 0.167 0.168 0.022 1 22.8 58.1 30324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 3.939 3.972 0.507 0.728 60.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 32.63 1.31 30307 1488 99.96 0.1738 0.1731 0.1862 0.1805
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 f_dihedral_angle_d 16.035 f_angle_d 0.902 f_chiral_restr 0.041 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1271 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing