3GO3
Interactions of an echinomycin-DNA complex with manganese(II) ions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6 | 24% V/V PEG 200, 6% W/V PEG 3350, 16MM MANGANESE(II) CHLORIDE, 20MM SPERMINE TETRACHLORIDE, 0.1M MES BUFFER (PH 6.0), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 58.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 26.544 | α = 90 |
b = 26.544 | β = 90 |
c = 162.129 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | MARMOSAIC 225 mm CCD | 2008-05-23 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | 2004-12-23 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | CCD | BRUKER SMART 6000 | 2005-12-21 | M | SAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | SLS | X10SA | |
2 | ROTATING ANODE | MACSCIENCE | |||
3 | ROTATING ANODE | MACSCIENCE |
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 | 1.1 | 30 | 92.2 | 0.0328 | 24.06 | 5.2 | 23140 | 1 |
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 | 1.1 | 1.2 | 76.5 | 0.2019 | 4.44 | 2.17 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | SAD | FREE R | 1.1 | 20 | 4 | 22400 | 1177 | 94.3 | 0.163 | 0.162 | 0.16 | 0.196 | 0.22 | RANDOM |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.229 |
s_zero_chiral_vol | 0.083 |
s_approx_iso_adps | 0.077 |
s_similar_adp_cmpnt | 0.065 |
s_non_zero_chiral_vol | 0.055 |
s_rigid_bond_adp_cmpnt | 0.05 |
s_anti_bump_dis_restr | 0.041 |
s_angle_d | 0.033 |
s_bond_d | 0.017 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 134 |
Nucleic Acid Atoms | 322 |
Solvent Atoms | 45 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
SHELXD | phasing |
SHELXL-97 | refinement |
XDS | data reduction |
SAINT | data reduction |
SADABS | data scaling |