8QZG
1,3 L,D-transpeptidase from Gluconobacter oxydans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.1M Imidazole MES monohydrate (acid) pH 6.5, 30 mM Magnesium chloride hexahydrate, 30 mM Calcium chloride dihydrate, 20% v/v PEG 500* MME; 10 % w/v PEG 20000 (Morpheus A1 condition) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 36.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.778 | α = 90 |
b = 56.688 | β = 90 |
c = 93.019 | 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 | 100 | PIXEL | DECTRIS EIGER X 9M | 2021-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8731 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.73 | 48.41 | 98.48 | 0.1108 | 0.997 | 10.48 | 5.6 | 29339 | 1.12 | 24.55 |
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 | 1.732 | 1.794 | 88.03 | 0.383 | 1.12 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.73 | 48.41 | 1.34 | 29296 | 1530 | 98.48 | 0.1722 | 0.1704 | 0.2048 | 27.1 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.5807 |
f_angle_d | 0.7723 |
f_chiral_restr | 0.0555 |
f_bond_d | 0.0085 |
f_plane_restr | 0.0085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2056 |
Nucleic Acid Atoms | |
Solvent Atoms | 133 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
XDS | data reduction |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |
PHENIX | refinement |