7QTG
Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GQW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 310 | Anaerobically: 60 % Tacsimate pH 7.0, 10 mM Imidazole, 30 mM NaCl, 1.5 mM Fe(II)SO4, 1.5 mM alpha-ketoglutarate, 1.5 mM ascorbate, 2.5 mM PL-CD6 (substrate) Cryo-protechtion: 10 % (2R,3R)-butane-2,3-diol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.03 | 59.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.923 | α = 90 |
b = 108.229 | β = 90 |
c = 65.373 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 225 mm CCD | 2009-08-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00630 | SLS | X06DA |
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 | 2.695 | 79.74 | 98.2 | 0.11 | 18.4 | 14.2 | 23401 |
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 | 2.7 | 2.84 | 100 | 1.022 | 14.9 |
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 | 1GQW | 2.695 | 79.74 | 23225 | 1166 | 97.6 | 0.242 | 0.2397 | 0.287 | RANDOM | 71.47 |
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] | |
-9.7423 | 7.8724 | 1.8699 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 18.34 |
t_omega_torsion | 3.02 |
t_angle_deg | 0.94 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4050 |
Nucleic Acid Atoms | |
Solvent Atoms | 35 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
autoPROC | data reduction |
Aimless | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |