4GJU
5-Methylcytosine modified DNA oligomer
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 0.04M sodium cacodylate buffer, 0.08M NaCl, 0.02M MgCl2, 0.012M spermine tetra hydrochloride, 35% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.495 | α = 90 |
b = 40.4 | β = 90 |
c = 65.5 | γ = 90 |
Symmetry | |
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Space Group | P 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 | PIXEL | DECTRIS PILATUS 2M-F | 2012-06-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00067 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.412 | 40.4 | 92.8 | 30.59 | 3.61 | 24635 | 22852 | 4 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.412 | 1.5 | 97.1 | 8.12 | 3.72 | 3958 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | FREE R | PDB ENTRY 1DPN | 1.412 | 40.4 | 2 | 4 | 24635 | 22852 | 1235 | 92.8 | 0.178 | 0.177 | 0.177 | 0.215 | RANDOM |
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] | |
Coordinate Error | ||
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Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
611 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.0636 |
s_angle_d | 0.0388 |
s_similar_adp_cmpnt | 0.0262 |
s_bond_d | 0.0183 |
s_non_zero_chiral_vol | 0.0156 |
s_anti_bump_dis_restr | 0.0141 |
s_rigid_bond_adp_cmpnt | 0.012 |
s_similar_dist | |
s_zero_chiral_vol | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 488 |
Solvent Atoms | 127 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
RemDAq | data collection |
PHASER | phasing |
SHELXL-97 | refinement |
XDS | data reduction |
XDS | data scaling |