3TG8
Mutant ribosomal protein L1 lacking ala158 from thermus thermophilus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1AD2 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 30 mM Tris-HCl, 75 mM NaCl with of 15% PEG 4K, 50 mM Tris-HCl, 0.2 M KBr (# 10 of Clear Strategy Screen I (MDL)) and 14% 2-methyl-2,4-pentandiol, 0.25 M MgCl2 in a 4:1:1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.15 | 42.9 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.628 | α = 90 |
b = 104.473 | β = 90 |
c = 64.287 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 2 2 21 |
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 | RAYONIX MX-225 | 2010-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.91841 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.95 | 40 | 97.9 | 0.099 | 0.087 | 11.94 | 3.94 | 15987 | 15656 | 23.44 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2.1 | 97.6 | 0.523 | 2.45 | 3.48 | 3129 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1AD2 | 1.95 | 32.144 | 1.99 | 15987 | 15652 | 783 | 97.94 | 0.1864 | 0.1843 | 0.2262 | 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] | |
-4.6853 | 4.8683 | -0.183 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.518 |
f_angle_d | 1.08 |
f_chiral_restr | 0.068 |
f_bond_d | 0.007 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1625 |
Nucleic Acid Atoms | |
Solvent Atoms | 89 |
Heterogen Atoms | 40 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data scaling |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |