6MT2
Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (I23 crystal form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4LUG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 292 | 4% Tacsimate pH 6.0, 12% PEG 3350 crystal after 3 months 20% Ethylene glycol as cryoprotectant MtPPA1 at 16.3 mg/ml |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.5 | 81.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 235.202 | α = 90 |
b = 235.202 | β = 90 |
c = 235.202 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | 2016-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0000 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.89 | 50 | 99.7 | 0.14 | 0.14 | 1 | 23.4 | 16 | 48141 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.89 | 3.07 | 98.2 | 1.7 | 1.8 | 0.65 | 1.9 | 15 |
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 | 4lug | 2.89 | 48.01 | 47082 | 1060 | 99.67 | 0.17278 | 0.17227 | 0.19529 | RANDOM | 83.382 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.748 |
r_dihedral_angle_3_deg | 17.796 |
r_dihedral_angle_4_deg | 16.887 |
r_long_range_B_refined | 7.371 |
r_long_range_B_other | 7.37 |
r_dihedral_angle_1_deg | 6.728 |
r_scangle_other | 4.989 |
r_mcangle_it | 4.475 |
r_mcangle_other | 4.475 |
r_scbond_it | 2.941 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5737 |
Nucleic Acid Atoms | |
Solvent Atoms | 77 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |
XDS | data scaling |