7W5S
A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | Ammonium Sulfate, HEPES pH 7.5, PEG 400, di-Potassium hydrogen phosphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.492 | α = 90 |
b = 72.33 | β = 90 |
c = 81.117 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CMOS | BRUKER PHOTON 100 | 2020-12-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | LIQUID ANODE | BRUKER METALJET | 1.34138 |
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 | 1.76 | 37.63 | 99.8 | 0.053 | 25.5 | 9.4 | 31366 |
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 | 1.76 | 1.79 | 0.193 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MIR | THROUGHOUT | 1.76 | 32.09 | 29286 | 1546 | 98.52 | 0.1502 | 0.1485 | 0.1815 | RANDOM | 14.608 |
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] | |
-5.82 | -4.13 | 9.96 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.014 |
r_dihedral_angle_4_deg | 18.33 |
r_dihedral_angle_3_deg | 13.847 |
r_dihedral_angle_1_deg | 6.739 |
r_angle_refined_deg | 1.787 |
r_angle_other_deg | 1.511 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2311 |
Nucleic Acid Atoms | |
Solvent Atoms | 359 |
Heterogen Atoms | 66 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
SADABS | data scaling |
PDB_EXTRACT | data extraction |
SAINT | data reduction |
PHENIX | phasing |