6OR9
Structure of L-lactate dehydrogenase from Trichoplusia ni
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | MCSG1 H11: 25% (W/V) PEG 3350, 200MM SODIUM CHLORIDE, 100MM HEPES FREE ACID / NAOH PH 7.5: TRNIA.00711.a.GL11.PS38300 AT 14.3 MG/ML + 2MM ATP: CRYO: 15% EG + BSI1767: TRAY 295240 H11: PUCK DAC0-8 FOR EXPERIMENTAL PHASING, A CRYSTAL FROM THE SAME DROP WAS INCUBATED FOR 15 SEC IN A SOLUTION OF 85% RESERVOIR AND 15% 2.5M SODIUM IODIDE IN ETHYLENE GLYCOL (FINAL IODIDE CONCENTRATION 375MM), AND VITRIFIED IN LIQUID NITROGEN: TRAY 295240H11: PUCK ANX5-15. THE PROTEIN WAS ACCIDENTALLY PURIFIED FROM A CULTURE THAT WAS SUPPOSED TO EXPRESS SSGCID PROTEIN PLFAA.18754.A.GL11., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.39 | α = 113.06 |
b = 76.48 | β = 109.84 |
c = 79.52 | γ = 88.7 |
Symmetry | |
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Space Group | P 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 | RAYONIX MX-300 | 2018-11-29 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2018-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.8 | 48.906 | 96.7 | 0.039 | 17.55 | 2.951 | 115247 | 30.18 |
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 | 1.8 | 1.85 | 93.1 | 0.344 | 2.74 | 2.68 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.8 | 48.91 | 1.98 | 115226 | 1971 | 97 | 0.159 | 0.158 | 0.195 | 0 | 29.42 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.316 |
f_angle_d | 0.87 |
f_chiral_restr | 0.06 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9055 |
Nucleic Acid Atoms | |
Solvent Atoms | 1097 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
PARROT | phasing |