3E1M
Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 298 | 1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. SUBSEQUENTLY, APO-BFR CRYSTALS WERE SOAKED IN A CRYOPROTECTANCT CONTAINING FE2+ AND BUFFERED USING MOPS PH 7 IN PLACE OF CITRATE PH 5. EXPOSURE TO IRON WAS LIMITED TO 2.5 MINUTES BEFORE FLASH FREEZING IN LIQUID NITROGEN. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.48 | 64.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 207.972 | α = 90 |
b = 207.972 | β = 90 |
c = 142.878 | γ = 90 |
Symmetry | |
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Space Group | P 42 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | 2006-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | SRS | PX10.1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.7 | 32 | 85.3 | 0.101 | 14.4 | 7.4 | 73181 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.7 | 2.85 | 46.8 | 0.225 | 4.7 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.7 | 32.04 | 69466 | 3678 | 85.1 | 0.242 | 0.241 | 0.259 | RANDOM | 5.87 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.39 | -0.39 | 0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.842 |
r_dihedral_angle_3_deg | 23.711 |
r_dihedral_angle_4_deg | 21.766 |
r_dihedral_angle_1_deg | 5.062 |
r_scangle_it | 2.845 |
r_scbond_it | 1.827 |
r_angle_refined_deg | 1.76 |
r_mcangle_it | 1.028 |
r_mcbond_it | 0.684 |
r_nbtor_refined | 0.323 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15804 |
Nucleic Acid Atoms | |
Solvent Atoms | 246 |
Heterogen Atoms | 374 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |