4AGZ
CRYSTAL STRUCTURE OF THE DB 985-D(CGCGAATTCGCG)2 COMPLEX AT 1.25 A RESOLUTION.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 285 | MAGNESIUM CHLORIDE, DNA, DB 985, MPD, SODIUM CACODYLATE BUFFER. PH 6.6, VAPOUR DIFFUSION, SITTING DROP, 285K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 61.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 24.026 | α = 90 |
b = 39.905 | β = 90 |
c = 65.784 | 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 | ADSC CCD | TOROIDAL MIRROR | 2009-07-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 1.25 | 39.9 | 99 | 0.05 | 17.3 | 6.5 | 18006 |
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 | 1.25 | 1.32 | 100 | 0.55 | 3.1 | 6.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1FQ2 | 1.25 | 14.76 | 17027 | 925 | 98.84 | 0.15755 | 0.15483 | 0.20704 | RANDOM | 12.92 |
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] | |
-0.12 | -0.12 | 0.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_bonded | 7.302 |
r_angle_other_deg | 4.559 |
r_scangle_it | 4.309 |
r_scbond_it | 3.329 |
r_rigid_bond_restr | 2.644 |
r_angle_refined_deg | 2.574 |
r_chiral_restr | 0.111 |
r_gen_planes_other | 0.037 |
r_gen_planes_refined | 0.034 |
r_bond_refined_d | 0.02 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 486 |
Solvent Atoms | 192 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |