4E2Z
X-ray Structure of the H225N mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and Sugar Product
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NDJ | PDB ENTRY 3NDJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 1.2-1.6 M sodium/potassium phosphate, 10 mM dTMP, 5 mM S-adenosyl-L-homocysteine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.9 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 102.039 | ¦Á = 90 |
b = 114.28 | ¦Â = 90 |
c = 38.038 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | Bruker Platinum 135 | Montel | 2011-05-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.4 | 38 | 93.6 | 0.076 | 0.076 | 10.5 | 4.3 | 87240 | 81683 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.4 | 1.5 | 80 | 0.323 | 0.323 | 2.16 | 2.15 | 13054 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3NDJ | 1.41 | 38 | 81651 | 77553 | 4098 | 93.73 | 0.19162 | 0.19027 | 0.2168 | RANDOM | 16.685 |
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] | |
-0.77 | 0.21 | 0.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.671 |
r_dihedral_angle_4_deg | 21.176 |
r_dihedral_angle_3_deg | 13.48 |
r_scangle_it | 7.573 |
r_dihedral_angle_1_deg | 6.329 |
r_scbond_it | 5.044 |
r_mcangle_it | 3.258 |
r_angle_refined_deg | 2.322 |
r_mcbond_it | 2.24 |
r_chiral_restr | 0.164 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3160 |
Nucleic Acid Atoms | |
Solvent Atoms | 461 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data collection |
PHASER | phasing |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |