5JVN
C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 285.15 | 17 % (w/v) PEG 4000, 15 % (w/v) glycerol, 85 mM HEPES (pH 7.5), 5 % (v/v) isopropanol, 10 mM phosphoenol pyruvate, 2.5 mM magnesium sulfate, 1 mM 2'-Br-dAppNHp |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4 | 68.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 249.43 | α = 90 |
b = 249.43 | β = 90 |
c = 84.06 | γ = 120 |
Symmetry | |
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Space Group | P 6 2 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 | PIXEL | DECTRIS PILATUS3 6M | Toroidal mirror | 2015-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.976252 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.9 | 49.54 | 99.9 | 0.089 | 0.999 | 13.9 | 6.9 | 34537 | 65.68 |
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 | 2.9 | 3.04 | 100 | 0.597 | 2.7 | 6.8 |
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 | 5JVL | 2.9 | 49.54 | 34536 | 1695 | 99.87 | 0.1996 | 0.1978 | 0.2352 | RANDOM | 90.5836 |
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] | |
1.68 | 0.84 | 1.68 | -5.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.861 |
r_dihedral_angle_4_deg | 15.835 |
r_dihedral_angle_3_deg | 14.07 |
r_dihedral_angle_1_deg | 4.788 |
r_angle_other_deg | 3.682 |
r_mcangle_it | 3.084 |
r_mcbond_it | 1.933 |
r_mcbond_other | 1.93 |
r_angle_refined_deg | 1.149 |
r_chiral_restr | 0.054 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6496 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
BUCCANEER | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |