5U7X
Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Vigna unguiculata subsp. cylindrica (Dolichos biflorus) in complex with phosphate and manganese
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5U7P |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 291 | 0.2 M MgCl2, 50 mM acetate, pH 5.0, 9-12% MPD, 10-2-% PEG 3350, 5 mM AMP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.09 | α = 90 |
b = 71.11 | β = 139.45 |
c = 93.27 | 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 | ADSC QUANTUM 315r | 2011-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
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 | 2.6 | 46.62 | 100 | 0.099 | 15.9 | 7.5 | 15843 | 30.59 |
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 | 5u7p | 2.6 | 46.62 | 15045 | 789 | 99.92 | 0.17191 | 0.16796 | 0.24804 | RANDOM | 31.664 |
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] | |
0.03 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.939 |
r_dihedral_angle_3_deg | 18.388 |
r_dihedral_angle_4_deg | 18.289 |
r_dihedral_angle_1_deg | 7.356 |
r_long_range_B_refined | 5.724 |
r_long_range_B_other | 5.668 |
r_scangle_other | 4.018 |
r_mcangle_it | 3.019 |
r_mcangle_other | 3.018 |
r_scbond_it | 2.528 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3147 |
Nucleic Acid Atoms | |
Solvent Atoms | 137 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |