4NFP
Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 8-aza-7-deaza-7-ethynyl Adenosine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294.15 | 10% MPD(v/v) (Drop), 35% MPD(v/v) (reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM SrCl2, 20mM MgCl2 hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.37 | 48.21 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 74.8 | α = 90 |
b = 43.19 | β = 120.82 |
c = 48.79 | 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 | CCD | ADSC QUANTUM 315 | 2012-07-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.127 | SSRL | BL7-1 |
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 | 1.85 | 35 | 91.3 | 0.029 | 18.04 | 2.7 | 11632 | 10615 |
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) | |||||||||||
1 | 1.85 | 1.9 | 75.4 | 0.33 | 2.32 | 1.85 | 858 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1.85 | 32.17 | 10615 | 10100 | 515 | 91.61 | 0.22364 | 0.22364 | 0.22222 | 0.2494 | RANDOM | 51.571 |
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] | |
2.81 | -1.81 | 4.53 | -3.65 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_angle_refined_deg | 1.894 |
r_angle_other_deg | 1.549 |
r_chiral_restr | 0.076 |
r_bond_other_d | 0.009 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.007 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1017 |
Solvent Atoms | 29 |
Heterogen Atoms | 9 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |