1IR0
OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM II)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FXB |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 6.5 | 277 | ammonium sulfate, MES, pH 6.5, MICRODIALYSIS, temperature 277.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.86 | 33.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.56 | α = 90 |
b = 30.38 | β = 124.02 |
c = 50.92 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 2000-05-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.55 | SPring-8 | BL41XU |
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 | 1 | 13.3 | 97.1 | 0.046 | 9.5 | 5.4 | 35329 | 35329 |
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 | 1.05 | 95.4 | 0.064 | 9.5 | 4 |
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 (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | 2FXB | 1 | 13.3 | 35328 | 35328 | 1765 | 97 | 0.112 | 0.112 | 0.112 | 0.11 | 0.139 | RANDOM |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
3 | 506 | 744 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.097 |
s_zero_chiral_vol | 0.089 |
s_anti_bump_dis_restr | 0.055 |
s_approx_iso_adps | 0.054 |
s_similar_adp_cmpnt | 0.037 |
s_angle_d | 0.029 |
s_from_restr_planes | 0.0261 |
s_bond_d | 0.014 |
s_rigid_bond_adp_cmpnt | 0.006 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 620 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 23 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
SHELXL-97 | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |