6FRM
Crystal Structure of coenzyme F420H2 oxidase (FprA) co-crystallized with 10 mM Tb-Xo4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OHH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | FprA native (about 90 % pure) at 43 g/l + 10 mM Xo4, crystallized at 291 K under anaerobic condition (95% N2 / 5% H2) in Combiclover Junior plate from Jena Bioscience. The protein was crystallized by mixing 1 ul protein of this mix with 1 ul of the mother liquor containing 20% w/v PEG 8000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate and 10 % v/v 2-propanol. Prior to freezing in liquid nitrogen, the crystal was soaked for few seconds in a cryo-protected solution containing: 20% w/v PEG 8000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate, 10 % v/v 2-propanol, 25 % v/v glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 49.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.17 | α = 90 |
b = 147.875 | β = 90.4 |
c = 146.059 | 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 | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-08-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.07227 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.19 | 48.69 | 99 | 0.044 | 9 | 6.7 | 181493 | 44.22 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.19 | 2.31 | 0.534 |
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 | 2OHH | 2.2 | 48.69 | 178580 | 8913 | 98.8 | 0.178 | 0.177 | 0.209 | RANDOM | 52.27 |
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] | |
-3.0461 | 2.1485 | 0.7493 | 2.2968 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 18.63 |
t_omega_torsion | 1.82 |
t_angle_deg | 1.16 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 25515 |
Nucleic Acid Atoms | |
Solvent Atoms | 1609 |
Heterogen Atoms | 343 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |