5IQU
WelO5 G166D variant bound to Fe(II), 2-oxoglutarate, and 12-epifischerindole U
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5IQS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 20% PEG 3350, 0.1 M Bis-tris pH 5.5, 0.1 M sodium acetate pH 4.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.107 | α = 90 |
b = 54.127 | β = 90.79 |
c = 74.639 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | MARMOSAIC 300 mm CCD | 2015-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 1.03 | APS | 21-ID-G |
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 | 2.5 | 50 | 99 | 0.056 | 9.7 | 3.6 | 8378 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.5 | 2.54 | 92.7 | 0.292 | 3.2 |
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 | 5IQS | 2.51 | 50 | 7919 | 459 | 81.31 | 0.225 | 0.2228 | 0.2619 | RANDOM | 50.748 |
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] | |
-2.67 | -0.06 | 5 | -2.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.753 |
r_dihedral_angle_3_deg | 14.29 |
r_dihedral_angle_4_deg | 10.771 |
r_dihedral_angle_1_deg | 6.099 |
r_mcangle_it | 2.617 |
r_mcbond_it | 1.485 |
r_mcbond_other | 1.485 |
r_angle_refined_deg | 1.039 |
r_angle_other_deg | 0.724 |
r_chiral_restr | 0.062 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2116 |
Nucleic Acid Atoms | |
Solvent Atoms | 35 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
HKL-2000 | data reduction |