6MT1
Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (R3 crystal form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 292 | 1.6% Tacsimate pH 5.0, 80 mM Na Citrate tribasic pH 5.6, 12.8% PEG 3350, 20% Glycerol Bromelain 5 ug/ml MtPPA1 7.7 mg/ml |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.784 | α = 90 |
b = 81.784 | β = 90 |
c = 176.935 | γ = 120 |
Symmetry | |
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Space Group | H 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 | PIXEL | DECTRIS PILATUS3 6M | 2017-04-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9793 | APS | 19-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 | 1.84 | 50 | 99.2 | 0.045 | 0.049 | 1 | 17.22 | 5.6 | 37764 |
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 | 1.84 | 1.95 | 95.7 | 0.87 | 0.96 | 0.79 | 1.7 | 5.4 |
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 | 1.84 | 40.89 | 36742 | 1020 | 99.17 | 0.16547 | 0.16449 | 0.20108 | RANDOM | 50.482 |
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] | |
0.77 | 0.39 | 0.77 | -2.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.202 |
r_dihedral_angle_4_deg | 14.494 |
r_dihedral_angle_3_deg | 13.584 |
r_dihedral_angle_1_deg | 7.232 |
r_long_range_B_refined | 6.669 |
r_long_range_B_other | 6.651 |
r_scangle_other | 4.528 |
r_mcangle_it | 3.207 |
r_mcangle_other | 3.206 |
r_scbond_it | 2.927 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2894 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |
XDS | data scaling |