4RK1
Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 294 | protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, cryoprotectant = reservoir + 30% w/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.33 | 63.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.371 | α = 90 |
b = 95.243 | β = 119.47 |
c = 123.602 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 315r | mirrors | 2014-09-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.9 | 50 | 100 | 0.1 | 0.1 | 16.9 | 5.2 | 197594 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 1.93 | 95.7 | 0.93 | 0.93 | 1.8 | 4.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.9 | 50 | 190152 | 5684 | 99.93 | 0.16012 | 0.15922 | 0.19234 | RANDOM | 37.347 |
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] | |
-1.34 | 0.03 | 2.63 | -0.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.251 |
r_long_range_B_other | 15.084 |
r_long_range_B_refined | 15.083 |
r_scangle_other | 14.268 |
r_scbond_it | 13.209 |
r_scbond_other | 13.208 |
r_dihedral_angle_3_deg | 12.763 |
r_dihedral_angle_4_deg | 9.884 |
r_mcangle_it | 8.621 |
r_mcangle_other | 8.621 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12715 |
Nucleic Acid Atoms | |
Solvent Atoms | 1175 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
ARP/wARP | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |