3BR5
Crystal Structure of the Complex of Rhodamine 6G Bound to QacR(E90Q), a Mutant of a Multidrug Binding Transcriptional Repressor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JT6 | PDB entry 1jt6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 273 | 1:1 10mg/ml protein with 2.3M Ammonium sulfate with 100mM Sodium Acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 67.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 171.726 | α = 90 |
b = 171.746 | β = 90 |
c = 94.785 | γ = 90 |
Symmetry | |
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Space Group | P 42 21 2 |
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 | NOIR-1 | Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror | 2007-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.0 | ALS | 4.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.8 | 49.03 | 100 | 0.061 | 18.1 | 7.52 | 31603 | 1.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.8 | 2.9 | 100 | 0.4 | 1.9 | 7.45 | 1517 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | PDB entry 1jt6 | 2.9 | 49.03 | 30359 | 30004 | 1599 | 98.83 | 0.24395 | 0.24395 | 0.24183 | 0.28449 | RANDOM | 65.546 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.548 |
r_dihedral_angle_3_deg | 16.633 |
r_dihedral_angle_4_deg | 8.451 |
r_dihedral_angle_1_deg | 4.986 |
r_scangle_it | 1.583 |
r_mcangle_it | 1.465 |
r_scbond_it | 0.972 |
r_angle_refined_deg | 0.907 |
r_mcbond_it | 0.784 |
r_angle_other_deg | 0.775 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5856 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 196 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
d*TREK | data reduction |
d*TREK | data scaling |
MOLREP | phasing |