2OML
crystal structure of E. coli pseudouridine synthase RluE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KSV | PDB entry 1KSV with N-terminal domain removed |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 294 | 4 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by microseeding a solution of 18-22% MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate and 2 mg/ml protein at pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 36.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.31 | α = 90 |
b = 56.78 | β = 90 |
c = 91.31 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 100 | CCD | ADSC QUANTUM 4 | double crystal monochrometer | 2003-06-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
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 | 1.2 | 40 | 98.1 | 0.063 | 13.7 | 4.6 | 52181 | -3 | -3 | 10.3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.2 | 1.24 | 94 | 0.713 | 2.1 | 3.5 | 4929 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB entry 1KSV with N-terminal domain removed | 1.2 | 28.08 | 49576 | 49576 | 4982 | 100 | 0.152 | 0.152 | 0.149 | 0.179 | RANDOM | 11.18 |
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] | |
-0.02 | 0.09 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.185 |
r_dihedral_angle_4_deg | 16.964 |
r_dihedral_angle_3_deg | 12.083 |
r_sphericity_free | 7.981 |
r_dihedral_angle_1_deg | 6.227 |
r_scangle_it | 4.705 |
r_scbond_it | 3.851 |
r_sphericity_bonded | 3.75 |
r_mcangle_it | 2.475 |
r_mcbond_it | 2.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1443 |
Nucleic Acid Atoms | |
Solvent Atoms | 191 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
CNS | phasing |