6VD0
Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with free Methionine and AMPCPP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 292 | 0.12 M Alcohols (1,6-hexanediol; 1-butanol; 1,2-propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol), 0.1 M HEPES and MOPS buffer at pH 7.5, 20% mmPEG500, 10% PEG 20000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.941 | α = 90 |
b = 84.721 | β = 95.67 |
c = 119.503 | 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 | 2018-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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 | 2 | 39.83 | 99.8 | 0.116 | 8.78 | 3.21 | 136621 | -3 |
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 | 2 | 2.07 | 99.1 | 0.375 | 2.13 | 2.41 |
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 | 6VCZ | 2 | 39.83 | 133001 | 2672 | 98.56 | 0.2226 | 0.222 | 0.2507 | RANDOM | 26.208 |
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] | |
0.05 | 0.09 | 0.08 | -0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.743 |
r_dihedral_angle_3_deg | 14.52 |
r_dihedral_angle_4_deg | 13.376 |
r_dihedral_angle_1_deg | 7.168 |
r_angle_refined_deg | 1.66 |
r_angle_other_deg | 1.353 |
r_chiral_restr | 0.085 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12053 |
Nucleic Acid Atoms | |
Solvent Atoms | 1201 |
Heterogen Atoms | 252 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
HKL-3000 | data reduction |
SCALEPACK | data scaling |