3LXY
Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 291 | 1 M Ammonium sulfate, 0.1 M Bis-Tris, 1% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.939 | α = 90 |
b = 88.105 | β = 90 |
c = 100.511 | γ = 90 |
Symmetry | |
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Space Group | C 2 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 | 100 | CCD | ADSC QUANTUM 315r | double crystal | 2010-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
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 | 1.7 | 35.52 | 97.8 | 0.075 | 18 | 4.3 | 37800 | 36631 | 2 | 2 |
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 | 1.7 | 1.73 | 83 | 0.61 | 2 | 3.6 | 1563 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1R8K | 1.7 | 35.52 | 2 | 2 | 36710 | 34771 | 1836 | 97.75 | 0.2 | 0.19421 | 0.19153 | 0.24794 | RANDOM | 20.103 |
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] | |
-1.78 | 3.79 | -2.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.102 |
r_dihedral_angle_4_deg | 15.809 |
r_dihedral_angle_3_deg | 15.42 |
r_dihedral_angle_1_deg | 6.095 |
r_scangle_it | 4.253 |
r_scbond_it | 2.833 |
r_angle_refined_deg | 1.875 |
r_mcangle_it | 1.787 |
r_mcbond_it | 1.13 |
r_angle_other_deg | 1.072 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2445 |
Nucleic Acid Atoms | |
Solvent Atoms | 187 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |