4IHS
Crystal Structure of BenM_DBD/catB site 1 DNA Complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3M1E | PDB entry 3M1E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER OIL | 6 | 288 | Equal volumes of precipitant, protein solution and DNA. Precipitant: sodium malonate Crystal Screen C4- 2.4 M sodium malonate pH 6.0. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.82 | 78.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 156.493 | α = 90 |
b = 156.493 | β = 90 |
c = 141.525 | 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 | MAR CCD 165 mm | 2008-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 0.99999 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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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 | 3.1 | 200 | 92.7 | 0.114 | 12.8 | 8.2 | 30569 | 99.4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.1 | 3.21 | 72.5 | 0.399 | 3 | 2350 |
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 3M1E | 3.1 | 48.95 | 30320 | 1523 | 91.97 | 0.1794 | 0.1782 | 0.2029 | RANDOM | 108.1734 |
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] | |
0.85 | 0.85 | -1.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.28 |
r_dihedral_angle_3_deg | 17.221 |
r_dihedral_angle_4_deg | 14.37 |
r_dihedral_angle_1_deg | 5.336 |
r_angle_refined_deg | 0.994 |
r_angle_other_deg | 0.843 |
r_chiral_restr | 0.062 |
r_gen_planes_refined | 0.005 |
r_bond_refined_d | 0.004 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2922 |
Nucleic Acid Atoms | 2038 |
Solvent Atoms | 20 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |