4RK0
Crystal structure of LacI family transcriptional regulator from Enterococcus faecalis V583, Target EFI-512923, with bound ribose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CTP | PDB ENTRY 3CTP |
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, 10 mM D-glucose, reservoir: 0.17 M sodium acetate, 0.085 M Tris-HCl, 8.5 25.5% w/v PEG4000, 15% w/v glycerol, cryoprotectant = reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.919 | α = 87.72 |
b = 77.234 | β = 82.57 |
c = 91.805 | γ = 84.33 |
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 | 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 | 1.8 | 50 | 97.7 | 0.097 | 0.097 | 17 | 4.4 | 93664 | -3 | 26.474 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.8 | 1.83 | 95.7 | 0.69 | 0.69 | 2.2 | 4.2 |
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 | MR | THROUGHOUT | PDB ENTRY 3CTP | 1.8 | 50 | 87918 | 2750 | 97.7 | 0.17168 | 0.16999 | 0.22271 | RANDOM | 38.826 |
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] | |
0.31 | -1.33 | -0.67 | 0.64 | 1.55 | -1.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.332 |
r_scbond_it | 19.292 |
r_scbond_other | 19.292 |
r_scangle_other | 18.433 |
r_long_range_B_other | 17.703 |
r_long_range_B_refined | 17.596 |
r_dihedral_angle_4_deg | 15.595 |
r_dihedral_angle_3_deg | 14.702 |
r_mcangle_other | 9.233 |
r_mcangle_it | 9.22 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8475 |
Nucleic Acid Atoms | |
Solvent Atoms | 445 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
PHASER | phasing |
ARP/wARP | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |