5VOO
Methionine synthase folate-binding domain with methyltetrahydrofolate from Thermus thermophilus HB8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 277 | 0.1 M sodium citrate pH 4.5, 22 % polyethylene glycol 3350, 0.2 M tri-sodium citrate, soaked with 6S-methyltetrahydrofolate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 188.463 | α = 90 |
b = 188.463 | β = 90 |
c = 247.137 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 EIGER X 16M | 2016-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.0332 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 2.4 | 163.21 | 99.4 | 0.092 | 0.048 | 0.996 | 8.93 | 4.5 | 100615 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.4 | 2.44 | 98.4 | 0.645 | 0.342 | 0.651 | 1.92 | 4.4 |
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 | 5VON | 2.4 | 163.21 | 95477 | 5056 | 99.29 | 0.19235 | 0.19039 | 0.22972 | RANDOM | 50.272 |
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] | |
0.35 | 0.18 | 0.35 | -1.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.384 |
r_dihedral_angle_4_deg | 16.284 |
r_dihedral_angle_3_deg | 13.683 |
r_long_range_B_other | 6.264 |
r_long_range_B_refined | 6.262 |
r_dihedral_angle_1_deg | 6.043 |
r_scangle_other | 4.526 |
r_mcangle_it | 3.726 |
r_mcangle_other | 3.726 |
r_scbond_it | 2.687 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13257 |
Nucleic Acid Atoms | |
Solvent Atoms | 322 |
Heterogen Atoms | 232 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |