5EQA
Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) with intermolecular cross-link between Lys158 and Cys245
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 292 | 30% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 10 mM magnesium acetate. Crystals were incubated overnight over the reservoir supplemented with 100 mM formaldehyde to complete cross-linking between Lys158 and Cys245 and vitrified in Paraton-N |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.24 | α = 90 |
b = 89.39 | β = 96.93 |
c = 92.24 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RAYONIX MX300-HS | 2015-10-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.7999 | APS | 22-ID |
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 | 1.32 | 40 | 99.9 | 0.065 | 12 | 5.1 | 234185 |
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 | 1.32 | 1.35 | 99.9 | 0.71 | 2 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.32 | 36.2 | 231842 | 2342 | 99.87 | 0.125 | 0.124 | 0.165 | RANDOM | 23.274 |
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] | |
0.74 | -0.29 | -0.02 | -0.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.946 |
r_sphericity_free | 36.321 |
r_sphericity_bonded | 15.491 |
r_dihedral_angle_4_deg | 14.744 |
r_dihedral_angle_3_deg | 13.36 |
r_dihedral_angle_1_deg | 6.178 |
r_long_range_B_refined | 5.687 |
r_long_range_B_other | 4.943 |
r_scangle_other | 4.505 |
r_rigid_bond_restr | 4.223 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7891 |
Nucleic Acid Atoms | |
Solvent Atoms | 1071 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |