7OWM
HsNMT1 in complex with both MyrCoA and HCPA substrate peptide GKQNSKLR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5O9T |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 20% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.879 | α = 90 |
b = 178.38 | β = 90 |
c = 58.255 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 mirrors | 2019-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.98400 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.5 | 48.773 | 98.4 | 0.115 | 0.032 | 0.9978 | 12.2 | 13.9 | 128545 | 16.7 |
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 | 1.5 | 1.54 | 97.8 | 1.532 | 0.541 | 0.6483 | 1.4 | 8.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5O9T | 1.5 | 48.77 | 1.35 | 128531 | 6514 | 96.04 | 0.1564 | 0.1544 | 0.1958 | 25.18 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.5748 |
f_angle_d | 0.8737 |
f_chiral_restr | 0.0597 |
f_bond_d | 0.0059 |
f_plane_restr | 0.0051 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6297 |
Nucleic Acid Atoms | |
Solvent Atoms | 1006 |
Heterogen Atoms | 213 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
STARANISO | data scaling |
Aimless | data scaling |
PHASER | phasing |