6Y1C
X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant D54F
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6H07 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7 | 293 | Protein solution (10 g/L LbADH , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl2 and precipitation buffer (1 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 100 g/L PEG 550 MME) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.76 | α = 90 |
b = 81.09 | β = 90 |
c = 113.13 | γ = 90 |
Symmetry | |
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Space Group | P 21 2 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 | 293 | PIXEL | DECTRIS EIGER X 16M | 2019-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0000089622351307 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.408 | 46.39 | 98 | 0.999 | 15.73 | 13.41 | 97917 |
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 | 1.408 | 1.44 | 94.5 | 0.606 |
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 | 6h07 | 1.41 | 46.39 | 93011 | 4897 | 97.92 | 0.1274 | 0.1256 | 0.1624 | RANDOM | 16.451 |
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] | |
0.26 | 0.87 | -1.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.597 |
r_dihedral_angle_4_deg | 23.4 |
r_dihedral_angle_3_deg | 11.541 |
r_dihedral_angle_1_deg | 6.807 |
r_angle_other_deg | 1.477 |
r_angle_refined_deg | 1.382 |
r_rigid_bond_restr | 1.218 |
r_chiral_restr | 0.071 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3748 |
Nucleic Acid Atoms | |
Solvent Atoms | 588 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |