2IGT
Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 295 | 0.1M sodium acetate 4.6, 3.2M sodium formate, 4% glycerol, 5mM SAM, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.941 | α = 90 |
b = 145.555 | β = 90 |
c = 204.895 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | ADSC QUANTUM 315 | mirrors | 2006-06-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID |
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 | 1.89 | 42.83 | 99.8 | 0.099 | 11.5 | 117.6 | 99837 | 99837 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.89 | 1.96 | 98.1 | 0.692 | 4.3 | 14.3 | 9691 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.89 | 42.83 | 89666 | 89666 | 10017 | 99.66 | 0.16534 | 0.16534 | 0.16231 | 0.19236 | RANDOM | 25.174 |
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] | |
0.67 | -1.33 | 0.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.01 |
r_dihedral_angle_4_deg | 19.075 |
r_dihedral_angle_3_deg | 15.066 |
r_dihedral_angle_1_deg | 6.65 |
r_scangle_it | 3.093 |
r_scbond_it | 2.044 |
r_angle_refined_deg | 1.396 |
r_mcangle_it | 1.291 |
r_mcbond_it | 0.874 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7395 |
Nucleic Acid Atoms | |
Solvent Atoms | 940 |
Heterogen Atoms | 138 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
HKL-3000 | phasing |
SHELXCD | phasing |
SHELXD | phasing |
SHELXE | model building |
SOLVE | phasing |
RESOLVE | phasing |
MLPHARE | phasing |
Coot | model building |
ARP/wARP | model building |