4R15
High-resolution crystal structure of Z-DNA in complex with Cr3+ cations
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 292 | A 1.5 MM WATER SOLUTION OF DNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE CRYSTAL WAS PLACED FOR SEVERAL DAYS IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM [CR(H2O)6]CL3, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.66 | 24.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 18.14 | α = 90 |
b = 30.44 | β = 90 |
c = 42.94 | 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 | CCD | RAYONIX MX-225 | 2011-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.91841 | BESSY | 14.2 |
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 | 0.97 | 24.83 | 98.4 | 0.016 | 24.85 | 2.53 | 26535 | 26535 | -3 | 13.586 |
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 | 0.973 | 1 | 93.2 | 0.432 | 2.05 | 2.14 |
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 (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 4HIF | 0.97 | 24.83 | 26535 | 1858 | 98.4 | 0.1447 | 0.1438 | 0.1438 | 0.1849 | 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 | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
13 | 136 | 280.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.096 |
s_similar_adp_cmpnt | 0.065 |
s_from_restr_planes | 0.0378 |
s_anti_bump_dis_restr | 0.029 |
s_angle_d | 0.028 |
s_bond_d | 0.019 |
s_rigid_bond_adp_cmpnt | 0.009 |
s_similar_dist | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 240 |
Solvent Atoms | 67 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
SHELXL-97 | refinement |
XDS | data reduction |
XSCALE | data scaling |