1KY8
Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | sodium formate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 185.2 | α = 90 |
b = 185.2 | β = 90 |
c = 132.1 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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 | IMAGE PLATE | MARRESEARCH | 1999-04-04 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 1999-01-01 | M | MAD | ||||||
3 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 1999-01-01 | M | MAD | ||||||
4 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 1999-01-01 | M | MAD | ||||||
1,2,3,4 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | 0.8469 | EMBL/DESY, HAMBURG | BW7B |
2 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.9796 | EMBL/DESY, HAMBURG | BW7A |
3 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.9792 | EMBL/DESY, HAMBURG | BW7A |
4 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.9724 | EMBL/DESY, HAMBURG | BW7A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | |||||||||
1,2,3,4 | 2.4 | 30 | 99.1 | 52004 | 52004 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2,3,4 | 2.4 | 2.5 | 100 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MAD | 2.4 | 30 | 52004 | 52004 | 2626 | 0.208 | 0.242 | random |
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 |
x_angle_deg | 1.48 |
x_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3772 |
Nucleic Acid Atoms | |
Solvent Atoms | 386 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
SHELX | model building |
X-PLOR | refinement |
SHELX | phasing |