8AB3
Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in complex with oxamate, NADH and FBP.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 18.5 % peg 3350 0.24 M sodium malonate dibasic monohydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.369 | α = 90 |
b = 111.504 | β = 99.78 |
c = 101.793 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS 2M | 2022-01-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.87313 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.616 | 100.314 | 99.3 | 0.1946 | 0.222 | 0.105 | 0.983 | 5.62 | 4.31 | 46537 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
2.616 | 2.661 | 100 | 0.7544 | 0.8525 | 0.3914 | 0.726 | 1.99 | 4.56 | 2342 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 4ojn | 2.616 | 100.31 | 46528 | 2317 | 99.3 | 0.1884 | 0.1862 | 0.2318 | RANDOM | 39.64 |
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] | |
15.5699 | 0.3017 | -8.3056 | -7.2643 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.55 |
t_omega_torsion | 2.85 |
t_angle_deg | 0.93 |
t_bond_d | 0.007 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9900 |
Nucleic Acid Atoms | |
Solvent Atoms | 491 |
Heterogen Atoms | 240 |
Software
Software | |
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Software Name | Purpose |
autoPROC | data processing |
XDS | data reduction |
Aimless | data scaling |
TRUNCATE | data processing |
BUSTER | refinement |
BUSTER | refinement |
PHENIX | phasing |