3DXJ
Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IW7 | PDB ENTRY 1IW7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.85 | 298 | MES, MAGNESIUM FORMATE, PEG 8000, SPERMINE, pH 5.85, VAPOR DIFFUSION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.69 | 73.78 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 235.09 | ¦Á = 90 |
b = 235.09 | ¦Â = 90 |
c = 250.88 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 108 | CCD | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
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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 | 50 | 96 | 0.11 | 10.8 | 3.7 | 150814 | -1 |
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) | |||||||||||
3 | 3.11 | 77.4 | 0.7 | 1.33 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MR | THROUGHOUT | PDB ENTRY 1IW7 | 3 | 50 | 298910 | 2351 | 96.3 | 0.235 | 0.235 | 0.289 | 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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_angle_deg | 1.57 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na | |
c_angle_deg_prot | |
c_dihedral_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 56018 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |