5VOP
Methionine synthase folate-binding domain from Thermus thermophilus HB8 native
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5VON |
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, 18 % polyethylene glycol 3350, 0.2 M tri-Sodium Citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.5 | 64.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.482 | α = 90 |
b = 111.482 | β = 90 |
c = 242.679 | 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 | 1.033 | 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 | 2.1 | 29.44 | 99.9 | 0.089 | 0.028 | 0.999 | 13.1 | 10.6 | 52825 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.1 | 2.16 | 99.9 | 0.75 | 0.238 | 0.909 | 1.9 | 10.2 |
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 | 2.1 | 29.44 | 50064 | 2667 | 99.88 | 0.19563 | 0.19424 | 0.22188 | RANDOM | 61.704 |
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] | |
1.69 | 0.84 | 1.69 | -5.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.493 |
r_dihedral_angle_4_deg | 15.147 |
r_dihedral_angle_3_deg | 12.391 |
r_long_range_B_refined | 7.291 |
r_long_range_B_other | 7.278 |
r_dihedral_angle_1_deg | 6.009 |
r_scangle_other | 5.599 |
r_mcangle_it | 4.38 |
r_mcangle_other | 4.38 |
r_scbond_it | 3.577 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4434 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |