8QAY
Medicago truncatula HISN5 (IGPD) in complex with MN, FMT, ACT, CIT, EDO, SO4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4MU0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 0.1 M carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, 0.2 M sodium oxamate); 1.0 M sodium HEPES, MOPS (acid), 40% glycerol, 20% w/v PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 58.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 137.6 | α = 90 |
b = 137.6 | β = 90 |
c = 265.65 | 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 | RIGAKU HyPix-6000HE | 2020-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU PhotonJet-R | 1.5418 |
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 | 2.2 | 80 | 98.8 | 0.192 | 0.234 | 0.986 | 5.72 | 2.99 | 93797 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.2 | 2.26 | 95 | 1.11 | 1.347 | 0.47 | 1.22 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.2 | 36.4 | 1.91 | 93704 | 937 | 98.7 | 0.1895 | 0.189 | 0.2314 | 37.06 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.2601 |
f_angle_d | 0.9294 |
f_chiral_restr | 0.0573 |
f_bond_d | 0.0074 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11480 |
Nucleic Acid Atoms | |
Solvent Atoms | 777 |
Heterogen Atoms | 176 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
PHASER | phasing |
PHENIX | refinement |
Coot | model building |
XDS | data scaling |