2I2X
Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 0.1 M sodium acetate, 0.05 M ammonium sulphate, 17% polyethyleneglycol, 15% glycerole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.75 | α = 90 |
b = 172.85 | β = 98.86 |
c = 190.54 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | ADSC QUANTUM 4 | mirrors | 2003-12-09 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | mirrors | 2003-09-15 | M | SINGLE WAVELENGTH | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9393 | ESRF | ID14-4 |
2 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | 1.2824 | MPG/DESY, HAMBURG | BW6 |
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 | ||||||||
1,2 | 2.5 | 20 | 95.3 | 0.133 | 9.4 | 2.6 | 218403 | 218403 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1,2 | 2.5 | 2.65 | 89.3 | 0.445 | 3.1 | 2.6 | 31920 |
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 | 2.5 | 20 | 207482 | 207482 | 10921 | 98.54 | 0.18426 | 0.18426 | 0.18179 | 0.23146 | RANDOM | 37.445 |
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] | |
0.78 | 1.12 | -0.9 | 0.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.893 |
r_dihedral_angle_4_deg | 21.059 |
r_dihedral_angle_3_deg | 18.556 |
r_dihedral_angle_1_deg | 5.755 |
r_scangle_it | 2.57 |
r_scbond_it | 1.575 |
r_angle_refined_deg | 1.385 |
r_mcangle_it | 1.037 |
r_mcbond_it | 0.549 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 43880 |
Nucleic Acid Atoms | |
Solvent Atoms | 946 |
Heterogen Atoms | 740 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
XDS | data reduction |
XDS | data scaling |
SHELXD | phasing |