3ZZN
5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase from Thermus thermophillus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 277 | 5-MUT TT-LDH WAS CRYSTALLIZED AT 10MG/ML BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD, FOLLOWING THE MIXING OF THE PROTEIN AND THE MOTHER-LIQUOR SOLUTIONS AT A 1:1 RATIO. THE MOTHER LIQUOR SOLUTION WAS 0.1 M HEPES BUFFER PH 9, 18-20% PEG 6000, 2 M LICL2, 500 MICROMOLAR ADP. CRYSTALS GREW WITHIN A WEEK AT 4 DEGREES CELSIUS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.123 | α = 90 |
b = 59.597 | β = 93.37 |
c = 153.076 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | CCD | ADSC CCD | 2009-05-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.9 | 45.53 | 96.8 | 0.103 | 14.25 | 3.47 | 30826 | 3 | 41.99 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.9 | 3 | 96.8 | 0.485 | 3.05 | 3.55 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 | PDB ENTRY 2V6M | 2.9 | 45.47 | 1.99 | 30812 | 2039 | 96.84 | 0.1919 | 0.1878 | 0.2512 |
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] | |
-0.2486 | -3.2788 | 1.8068 | -1.5582 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.057 |
f_angle_d | 1.704 |
f_chiral_restr | 0.107 |
f_plane_restr | 0.016 |
f_bond_d | 0.015 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9135 |
Nucleic Acid Atoms | |
Solvent Atoms | 416 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |