6IAF
Fifteen minutes iron loaded Rana Catesbeiana H' ferritin variant H54N
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4LQH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 281 | 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.72 | α = 90 |
b = 183.72 | β = 90 |
c = 183.72 | γ = 90 |
Symmetry | |
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Space Group | F 4 3 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 | MARMOSAIC 225 mm CCD | 2012-10-08 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M | 2012-10-29 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M | 2012-10-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.95372 | ESRF | BM14 |
2 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.73893 | ELETTRA | 5.2R |
3 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.76116 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.35 | 22.44 | 100 | 0.073 | 0.078 | 0.021 | 22.3 | 14.2 | 58512 | 2 | 9.93 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.35 | 1.42 | 100 | 0.447 | 0.48 | 0.128 | 6 | 13.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4LQH | 1.35 | 22.44 | 55550 | 2960 | 99.94 | 0.11465 | 0.11326 | 0.14072 | RANDOM | 10.748 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.644 |
r_dihedral_angle_4_deg | 20.392 |
r_dihedral_angle_3_deg | 13.33 |
r_dihedral_angle_1_deg | 4.547 |
r_long_range_B_refined | 3.372 |
r_long_range_B_other | 2.025 |
r_scangle_other | 1.759 |
r_rigid_bond_restr | 1.624 |
r_angle_other_deg | 1.585 |
r_angle_refined_deg | 1.481 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1413 |
Nucleic Acid Atoms | |
Solvent Atoms | 361 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |