2P5L
Crystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2P5K | N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS) |
experimental model | PDB | 1JFS | N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.1 | 277 | 1.7M ammonium sulphate, 0.1M HEPES, 0.1M sodium chloride, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.10 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.77 | 74.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 139.105 | α = 90 |
b = 118.77 | β = 90 |
c = 121.23 | γ = 90 |
Symmetry | |
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Space Group | I 21 21 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 4 | MIRRORS | 2003-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.2 | SRS | PX14.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.85 | 24.81 | 98 | 0.063 | 0.063 | 18 | 4.1 | 23191 | 75.5 |
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 | 2.85 | 3 | 98 | 0.406 | 0.406 | 3.4 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS) | 2.85 | 24.81 | 23191 | 1198 | 97.5 | 0.208 | 0.207 | 0.231 | RANDOM | 23.9 |
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] | |
-0.89 | 0.53 | 0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.998 |
r_dihedral_angle_4_deg | 23.381 |
r_dihedral_angle_3_deg | 18.637 |
r_dihedral_angle_1_deg | 5.263 |
r_angle_refined_deg | 1.675 |
r_mcangle_it | 1.173 |
r_scangle_it | 0.874 |
r_mcbond_it | 0.695 |
r_scbond_it | 0.587 |
r_nbtor_refined | 0.346 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2064 |
Nucleic Acid Atoms | 1448 |
Solvent Atoms | 13 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |