2NQZ
Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaza-7-aminomethyl-guanine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Y5X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | 100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, 14mg/ml TGT, 20mM preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.9 | α = 90 |
b = 64.93 | β = 96.36 |
c = 71.18 | 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 | 113 | IMAGE PLATE | RIGAKU RAXIS IV | mirrors | 2004-09-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.46 | 20 | 98.6 | 0.044 | 18 | 3.2 | 64991 | 64991 |
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 | FREE R | 1Y5X | 1.46 | 8 | 64991 | 64991 | 38064 | 92.3 | 0.1515 | 0.15 | 0.15 | 0.1984 | RANDOM |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
31 | 2827 | 3365 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.084 |
s_zero_chiral_vol | 0.072 |
s_non_zero_chiral_vol | 0.067 |
s_similar_adp_cmpnt | 0.051 |
s_anti_bump_dis_restr | 0.034 |
s_angle_d | 0.031 |
s_from_restr_planes | 0.0284 |
s_bond_d | 0.011 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2739 |
Nucleic Acid Atoms | |
Solvent Atoms | 258 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
CNS | refinement |
SHELXL | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |