5OK4
Crystal structure of native [Fe]-hydrogenase Hmd from Methanothermobacter marburgensis inactivated by O2.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2JJF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 281.15 | 1-ml mixture containing 120 mM potassium phosphate pH 6.0, 1 mM EDTA, 26 uM (1 mg/ml) [Fe]-hydrogenase and 26 uM methylene-H4MPT was incubated in 5-ml amber vials with rubber stoppers under a gas mixture of N2/O2/H2 (70%/20%/10%) at 40 degree Celsius for 1 h. The inactivated enzyme was concentrated to 25 mg/ml using a 30 kDa centrifugal filter (Millipore). 0.7-ul of 25 mg/ml O2-inactivated [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, and 200 mM LiSO4. The best diffracting crystal was obtained in one month. Prior to freezing the crystal was soaked for 3 seconds in 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, 200 mM LiSO4 and 30% glycerol v/v. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.93 | 58.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.418 | α = 90 |
b = 127.418 | β = 90 |
c = 141.211 | γ = 120 |
Symmetry | |
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Space Group | H 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 | PIXEL | DECTRIS PILATUS 6M | 2016-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.00005 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.29 | 47.07 | 100 | 0.048 | 0.018 | 1 | 19.6 | 8.2 | 110077 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.29 | 1.36 | 100 | 1.128 | 0.423 | 0.638 | 1.9 | 8 |
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 (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2JJF | 1.29 | 43.474 | 1.34 | 110053 | 5448 | 99.95 | 0.128 | 0.127 | 0.1471 | 21 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 24.265 |
f_angle_d | 1.194 |
f_chiral_restr | 0.086 |
f_bond_d | 0.01 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2639 |
Nucleic Acid Atoms | |
Solvent Atoms | 516 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |