2G1P
Structure of E. coli DNA adenine methyltransferase (DAM)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 289 | 100 mM KCl, 10 mM MgSO4, 5-15% PEG400, 100 mM MES or HEPES (pH 6.6-7.4), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.2 | α = 90 |
b = 71.3 | β = 90.03 |
c = 97.8 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARRESEARCH | 2005-04-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97179 | APS | 22-ID |
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 | 1.89 | 33.6 | 99.9 | 0.102 | 9.1 | 7.4 | 51126 | 51126 | -3 | 18.5 |
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 | 1.89 | 1.92 | 98.7 | 0.575 |
Refinement
Statistics | |||||||||||||||||||
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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 | Modified PDB entry 2DPM | 1.89 | 33.6 | 51126 | 51126 | 2437 | 99.9 | 0.188 | 0.188 | 0.188 | 0.216 | RANDOM | 29.8 |
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] | |
12.07 | -9 | -3.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22 |
c_scangle_it | 2.82 |
c_scbond_it | 1.95 |
c_mcangle_it | 1.58 |
c_angle_deg | 1.4 |
c_improper_angle_d | 1.01 |
c_mcbond_it | 1.01 |
c_bond_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4001 |
Nucleic Acid Atoms | 486 |
Solvent Atoms | 314 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
GLRF | phasing |
CNS | refinement |
HKL-2000 | data reduction |