7W5V
A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 7W5S |
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 | |
---|---|
Matthews coefficient | Solvent content |
2.24 | 45.17 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 52.424 | α = 90 |
b = 72.397 | β = 90 |
c = 81.368 | γ = 90 |
Symmetry | |
---|---|
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 | 2021-07-02 | 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 | 1.81 | 36.2 | 99.5 | 0.072 | 13.6 | 6.39 | 28970 |
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 | 1.81 | 1.84 | 0.353 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 7W5S | 1.81 | 36.2 | 27250 | 1441 | 99.28 | 0.1696 | 0.1672 | 0.2154 | RANDOM | 19.95 |
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] | |
-7.9 | -9.17 | 17.08 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.449 |
r_dihedral_angle_4_deg | 19.616 |
r_dihedral_angle_3_deg | 14.514 |
r_dihedral_angle_1_deg | 7.005 |
r_angle_refined_deg | 1.775 |
r_angle_other_deg | 1.476 |
r_chiral_restr | 0.086 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2311 |
Nucleic Acid Atoms | |
Solvent Atoms | 280 |
Heterogen Atoms | 63 |
Software
Software | |
---|---|
Software Name | Purpose |
SADABS | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SAINT | data reduction |
REFMAC | phasing |