6ZMC
Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000 bar using the high pressure freezing method
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ITB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 294 | protein : 20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl reservoir : 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.388 | α = 90 |
b = 51.909 | β = 90.36 |
c = 78.978 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | PIXEL | DECTRIS PILATUS3 S 6M | 2018-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 1.770 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 2.5 | 50 | 99.3 | 0.065 | 0.999 | 16.5 | 6.2 | 16699 | 2.2 | 72.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.65 | 97.7 | 0.79 | 0.912 | 2.24 | 6.01 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2ITB | 2.5 | 47.52 | 15868 | 829 | 99.33 | 0.1849 | 0.1817 | 0.2446 | RANDOM | 69.561 |
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] | |
-5.55 | -3.97 | 2.01 | 3.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.742 |
r_dihedral_angle_4_deg | 18.659 |
r_dihedral_angle_3_deg | 17.557 |
r_dihedral_angle_1_deg | 5.816 |
r_angle_refined_deg | 1.443 |
r_angle_other_deg | 1.25 |
r_chiral_restr | 0.06 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3155 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |