1M69
Atomic Resolution Structure of 5Br-9amino-DACA with d[CGTACG]2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 366D | ddf073 structure, with corrected sequence |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290.15 | Ammonium acetate, magnesium acetate, sodium cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 55.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.186 | α = 90 |
b = 30.186 | β = 90 |
c = 39.443 | γ = 120 |
Symmetry | |
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Space Group | P 64 |
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 | 2001-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.8068 | EMBL/DESY, HAMBURG | X11 |
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 | 1.1 | 10 | 94.72 | 8308 | 4 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.1 | 1.15 | 95.79 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | ddf073 structure, with corrected sequence | 1.1 | 10 | 4 | 7900 | 7350 | 408 | 94.8 | 0.1325 | 0.1325 | 0.1325 | 0.1864 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
7 | 81 | 190.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_dist | 0.07 |
s_similar_adp_cmpnt | 0.046 |
s_bond_d | 0.037 |
s_anti_bump_dis_restr | 0.015 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_from_restr_planes | 0.0028 |
s_angle_d | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 120 |
Solvent Atoms | 37 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
XDS | data reduction |
SHELX | model building |
SHELXL-97 | refinement |
XDS | data scaling |
SHELX | phasing |