5C4D
Crystal structure of GTB + UDP-Glc + DI
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LZ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5 mM manganese chloride. Grown 5-10 days. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.64 | α = 90 |
b = 149.58 | β = 90 |
c = 79.23 | 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 | 113 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2007-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 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 | 1.4 | 74.79 | 98.1 | 0.033 | 21.5 | 4.16 | 60723 |
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 | 1.4 | 1.45 | 87.1 | 0.278 | 3.3 | 2.46 | 5307 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1LZ7 | 1.4 | 74.79 | 57638 | 3083 | 98.07 | 0.1761 | 0.1754 | 0.1887 | RANDOM | 17.525 |
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] | |
-0.36 | 0.15 | 0.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.636 |
r_dihedral_angle_4_deg | 18.353 |
r_dihedral_angle_3_deg | 12.323 |
r_dihedral_angle_1_deg | 6.448 |
r_mcangle_it | 1.8 |
r_angle_refined_deg | 1.511 |
r_mcbond_it | 1.122 |
r_mcbond_other | 1.115 |
r_angle_other_deg | 0.976 |
r_chiral_restr | 0.089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2277 |
Nucleic Acid Atoms | |
Solvent Atoms | 272 |
Heterogen Atoms | 71 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Coot | model building |
PHASER | phasing |
CrystalClear | data reduction |