4EK2
The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4DUT | PDB ENTRY 4DUT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | ButhA.00438.a.A1 PS01186 at 42.64 mg/mL in 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 10 mM dAMP, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.68 | α = 90 |
b = 90.68 | β = 90 |
c = 90.43 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | CCD | RIGAKU SATURN 944 | 2012-02-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 40.553 | 97.2 | 0.066 | 30.21 | 25415 | -3 | 19.831 |
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 | 2.05 | 84.4 | 0.219 | 7.95 |
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 | PDB ENTRY 4DUT | 2 | 40.553 | 25383 | 1295 | 97.22 | 0.1916 | 0.1897 | 0.2282 | RANDOM | 16.6122 |
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] | |
-0.24 | -0.24 | 0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.722 |
r_dihedral_angle_4_deg | 18.641 |
r_dihedral_angle_3_deg | 14.022 |
r_dihedral_angle_1_deg | 5.729 |
r_scangle_it | 3.149 |
r_scbond_it | 1.885 |
r_angle_refined_deg | 1.332 |
r_mcangle_it | 1.103 |
r_angle_other_deg | 0.923 |
r_mcbond_it | 0.615 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2162 |
Nucleic Acid Atoms | |
Solvent Atoms | 275 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |