6VCX
Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 1 (AtMAT1)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 292 | 1.8 M (NH4)2SO4, 0.08 M Bis-Tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.722 | α = 90 |
b = 68.096 | β = 90 |
c = 209.697 | γ = 90 |
Symmetry | |
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Space Group | I 21 21 21 |
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 | 2018-05-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.000 | APS | 22-BM |
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 | 1.1 | 48.78 | 96.2 | 0.049 | 20.51 | 7.38 | 160169 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.1 | 1.17 | 92.8 | 0.351 | 4.91 | 7.36 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | D_1000245963 | 1.1 | 48.78 | 158566 | 1602 | 96.23 | 0.1109 | 0.1106 | 0.1353 | RANDOM | 13.017 |
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] | |
-1.12 | -0.02 | 1.14 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.424 |
r_dihedral_angle_4_deg | 14.068 |
r_dihedral_angle_3_deg | 13.156 |
r_dihedral_angle_1_deg | 6.713 |
r_rigid_bond_restr | 4.727 |
r_angle_refined_deg | 1.79 |
r_angle_other_deg | 1.577 |
r_chiral_restr | 0.108 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2975 |
Nucleic Acid Atoms | |
Solvent Atoms | 551 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
XDS | data reduction |
XSCALE | data scaling |