8SSD
Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277.15 | 0.1 M Sodium Acetate, pH 4.6, 2 M Sodium Formate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.177 | α = 90 |
b = 96.177 | β = 90 |
c = 356.04 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 | PIXEL | DECTRIS EIGER X 16M | K-B pair of biomorph mirrors for vertical and horizontal focusing, with two horizontally deflecting mirrors | 2022-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.033 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 40.55 | 100 | 0.177 | 0.187 | 0.061 | 0.991 | 8.1 | 9.4 | 76051 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.4 | 2.45 | 100 | 0.903 | 0.954 | 0.306 | 0.667 | 9.6 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3BUL | 2.4 | 39.85 | 75947 | 3829 | 99.9 | 0.265 | 0.301 | RANDOM | 44.88 |
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] | |
-4.612 | -4.612 | 9.224 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 14.493 |
r_dihedral_angle_2_deg | 10.455 |
r_dihedral_angle_1_deg | 7.589 |
r_mcangle_it | 4.176 |
r_mcangle_other | 4.175 |
r_scangle_it | 3.958 |
r_scangle_other | 3.958 |
r_mcbond_it | 2.622 |
r_mcbond_other | 2.621 |
r_scbond_it | 2.423 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11959 |
Nucleic Acid Atoms | |
Solvent Atoms | 485 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |