4DF3
Crystal Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 296.15 | 20mM Tris.HCL pH8, 150mM NaCl, 200mM Imidazole, 20mM Tris.HCl pH7, 5% Isopropanol, 10% PEG 4000, pH 6.5, Vapor DIffusion, Sitting Drop, temperature 296.15K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.22 | 44.5 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 39.639 | α = 66.28 |
b = 52.087 | β = 84.55 |
c = 63.03 | γ = 77.61 |
Symmetry | |
---|---|
Space Group | P 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 | RIGAKU SATURN 92 | 2007-05-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54187 |
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 | 1.73 | 46.78 | 90.6 | 0.066 | 0.189 | 9.1 | 47059 | 2 | 1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.73 | 46.78 | 40488 | 2163 | 90.64 | 0.18954 | 0.1871 | 0.2335 | RANDOM | 21.715 |
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] | |
0.05 | -0.06 | -0.09 | 0.08 | -0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.392 |
r_dihedral_angle_4_deg | 21.415 |
r_dihedral_angle_3_deg | 13.027 |
r_dihedral_angle_1_deg | 6.333 |
r_scangle_it | 5.649 |
r_scbond_it | 3.59 |
r_mcangle_it | 2.318 |
r_angle_refined_deg | 1.907 |
r_mcbond_it | 1.376 |
r_chiral_restr | 0.143 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3694 |
Nucleic Acid Atoms | |
Solvent Atoms | 334 |
Heterogen Atoms | 54 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
CrystalClear | data collection |
d*TREK | data reduction |
d*TREK | data scaling |
CNS | phasing |