6L2M
The structure of the tRNA-specific deaminase mutant from M. capricolum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6L2L |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 1.4M ammonium sulfate, 0.1M Sodium citrate pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 59.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.589 | α = 90 |
b = 55.589 | β = 90 |
c = 109.227 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 2019-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.979 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.3 | 50 | 100 | 0.105 | 0.99 | 38.5 | 18.7 | 9158 | 42.6410606465 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.38 | 100 | 0.51 | 0.969 | 4.8 | 18.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6L2L | 2.30254929158 | 48.141486171 | 1.38105400115 | 9119 | 469 | 99.7811576759 | 0.201104412273 | 0.198421847872 | 0.251408846831 | 48.0589077702 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.4852966091 |
f_angle_d | 0.812726388142 |
f_chiral_restr | 0.0540661923588 |
f_bond_d | 0.00729693315512 |
f_plane_restr | 0.00428985158862 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1147 |
Nucleic Acid Atoms | |
Solvent Atoms | 38 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |