4V7S
Crystal structure of the E. coli ribosome bound to telithromycin.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3I1M | PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P |
experimental model | PDB | 3I1N | PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P |
experimental model | PDB | 3I1O | PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P |
experimental model | PDB | 3I1P | PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.5 | 291 | PEG8k, MPD, pH 6.5, microbatch, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.34 | 63.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 210.759 | α = 90 |
b = 433.272 | β = 90 |
c = 618.863 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.1 | ALS | 8.3.1 |
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 | 3.25 | 100 | 91.2 | 0.083 | 15.2 | 2.5 | 801811 | 801811 | 2 | 2 |
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 | 3.25 | 3.31 | 81.1 | 0.455 | 1.8 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | PDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P | 3.2547 | 85.218 | 0.02 | 754750 | 754750 | 15234 | 85.76 | 0.1943 | 0.1933 | 0.245 |
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] | |
-2.2555 | -12.542 | 9.4561 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.323 |
f_angle_d | 0.923 |
f_chiral_restr | 0.063 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 18554 |
Nucleic Acid Atoms | 32895 |
Solvent Atoms | 208 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHENIX | refinement |