2VZ4
The N-terminal domain of MerR-like protein TipAL bound to promoter DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1R8D | PDB ENTRY 1R8D |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | SITTING DROP CONTAINING 4 MICROLITERS PROTEIN-DNA SOLUTION PLUS 6 MICROLITERS RESERVOIR SOLUTION. PROTEIN-DNA SOLUTION: 500 MICROMOLAR (6 MILLIGRAMS/MILLILITER) PROTEIN, 275 MICROMOLAR DOUBLE-STRANDED DNA, 123 MILLIMOLAR SODIUM CHLORIDE, 16 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), 8 MILLIMOLAR SODIUM CACODYLATE, 4 MILLIMOLAR MAGNESIUM CHLORIDE, 0.8 MILLIMOLAR EDTA (ETHYLENEDIAMINETETRAACETIC ACID), PH 8. RESERVOIR SOLUTION: 15% (WEIGHT/VOLUME) PEG-8K (POLY(ETHYLENE GLYCOL) WITH MOLECULAR MASS 8000 GRAMS/MOLE), 200 MILLIMOLAR MAGNESIUM CHLORIDE, 100 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), PH 8.5. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.83 | 60 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 45.85 | α = 90 |
b = 67.467 | β = 90 |
c = 73.129 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2005-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.9 | 72.74 | 99.5 | 0.08 | 20.2 | 6.3 | 5321 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.9 | 3.06 | 99.5 | 0.35 | 5.5 | 6.1 |
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 | PDB ENTRY 1R8D | 2.9 | 30 | 4922 | 230 | 95.9 | 0.24 | 0.239 | 0.274 | RANDOM | 47.66 |
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] | |
1.5 | -4.37 | 2.87 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.988 |
r_dihedral_angle_4_deg | 18.876 |
r_dihedral_angle_3_deg | 15.313 |
r_dihedral_angle_1_deg | 5.115 |
r_scangle_it | 5.019 |
r_scbond_it | 3.359 |
r_mcangle_it | 2.385 |
r_mcbond_it | 1.519 |
r_angle_refined_deg | 1.337 |
r_angle_other_deg | 0.912 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 794 |
Nucleic Acid Atoms | 428 |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |