7PK2
Bovine Glycine N-Acyltransferase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | 0.2 M sodium malonate, 20% w/v polyethylene glycol 3,350, pH 5.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.112 | α = 90 |
b = 63.587 | β = 90 |
c = 135.503 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 93 | PIXEL | DECTRIS EIGER2 X 16M | 2020-10-15 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 45 | PIXEL | DECTRIS PILATUS 12M | 2021-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9762 | Diamond | I03 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 2.755 | Diamond | I23 |
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 | 1.25 | 37.37 | 97.22 | 0.043 | 0.047 | 0.018 | 1 | 16.2 | 6.8 | 146947 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.25 | 1.25 | 0.4 | 1.18 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.25 | 37.37 | 139600 | 7348 | 97.21 | 0.1779 | 0.1768 | 0.1997 | RANDOM | 23.2609 |
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 | 0.88 | -1.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
TORSION ANGLES. PERIOD 2 (DEGREES) | 34.109 |
TORSION ANGLES. PERIOD 4 (DEGREES) | 20.582 |
TORSION ANGLES. PERIOD 3 (DEGREES) | 13.853 |
TORSION ANGLES. PERIOD 1 (DEGREES) | 6.521 |
r_angle_refined_deg | 1.754 |
r_angle_other_deg | 1.45 |
r_chiral_restr | 0.092 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4588 |
Nucleic Acid Atoms | |
Solvent Atoms | 433 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
xia2 | data reduction |
XSCALE | data scaling |
SHELXD | phasing |
CRANK2 | phasing |
HKL2Map | model building |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |