5Z5C
Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 24% (W/V) PEG 3350, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.76 | α = 90 |
b = 136.16 | β = 90 |
c = 171.68 | γ = 90 |
Symmetry | |
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Space Group | P 2 21 21 |
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 | 95 | CCD | ADSC QUANTUM 210r | 2011-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1 | Photon Factory | AR-NW12A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.07 | 42.66 | 99.6 | 0.051 | 22.3 | 7 | 83053 |
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 | 2.07 | 2.12 | 98.4 | 0.245 | 7.2 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.07 | 40.93 | 78808 | 4180 | 99.47 | 0.18839 | 0.18561 | 0.24177 | RANDOM | 38.583 |
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] | |
0.91 | 1.63 | -2.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.656 |
r_dihedral_angle_4_deg | 13.91 |
r_dihedral_angle_3_deg | 13.832 |
r_dihedral_angle_1_deg | 6.804 |
r_long_range_B_refined | 3.109 |
r_long_range_B_other | 3.107 |
r_scangle_other | 1.915 |
r_mcangle_it | 1.633 |
r_mcangle_other | 1.633 |
r_angle_refined_deg | 1.597 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10401 |
Nucleic Acid Atoms | |
Solvent Atoms | 373 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |