1EN9
1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5DNB | BDJ019 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 275 | initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate 0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.06 | 36.88 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 32.243 | α = 90 |
b = 25.352 | β = 117.17 |
c = 34.19 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | AREA DETECTOR | MARRESEARCH | 1998-11-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X8C | NSLS | X8C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 0.985 | 8 | 93.3 | 0.031 | 32.8 | 4.87 | 13087 | 13087 | -1 | 5.82 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
0.985 | 1.016 | 89.5 | 0.122 | 6.9 | 1253 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | BDJ019 | 0.985 | 8 | 13087 | 13087 | 654 | 93.3 | 0.1405 | 0.1405 | 0.1509 | 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 |
9 | 113 | 271.4 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_angle_d | 0.053 |
s_anti_bump_dis_restr | 0.041 |
s_approx_iso_adps | 0.039 |
s_similar_adp_cmpnt | 0.023 |
s_bond_d | 0.018 |
s_rigid_bond_adp_cmpnt | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 385 |
Solvent Atoms | 51 |
Heterogen Atoms | 48 |
Software
Software | |
---|---|
Software Name | Purpose |
X-PLOR | model building |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |