4R0V
[FeFe]-hydrogenase Oxygen Inactivation is Initiated by the Modification and Degradation of the H cluster 2Fe Subcluster
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3LX4 | PDB entry 3lx4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.5 | 298 | 25.5% Polyethylene Glycol 8,000, 0.085 M Sodium Cacodylate, 0.17 M Sodium Acetate Trihydrate, 1mM Sodium Dithionite, pH 6.5, SMALL TUBES, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.645 | α = 90 |
b = 70.964 | β = 91.91 |
c = 94.686 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 77 | PIXEL | DECTRIS PILATUS 6M | 2013-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 1.73450 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.29 | 94.633 | 88.2 | 46625 | 41114 | 2 | 3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.29 | 2.41 | 12 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | PDB entry 3lx4 | 2.29 | 35 | 3 | 46625 | 39011 | 2097 | 88.17 | 0.20882 | 0.2065 | 0.25211 | RANDOM | 49.48 |
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] | |
1.78 | -0.01 | -1.65 | -0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.337 |
r_dihedral_angle_4_deg | 18.233 |
r_dihedral_angle_3_deg | 17.247 |
r_long_range_B_refined | 8.401 |
r_long_range_B_other | 8.343 |
r_dihedral_angle_1_deg | 7.298 |
r_scangle_other | 5.547 |
r_mcangle_it | 4.491 |
r_mcangle_other | 4.491 |
r_scbond_other | 3.924 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6282 |
Nucleic Acid Atoms | |
Solvent Atoms | 293 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |