3DMH
T. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in complex with AdoMet and Guanosine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | microbatch technique under oil | 8.5 | 277 | 0.085 M TRIS HCl (pH 8.5), 25.5% w/v PEG4000 15% glycerol, microbatch technique under oil, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.863 | α = 90 |
b = 86.234 | β = 90 |
c = 95.091 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MAR CCD 165 mm | Slits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m. | 2008-04-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.9797 | NSLS | X4C |
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 | 1.55 | 30 | 97.8 | 0.066 | 23.8 | 5.7 | 57244 |
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 | 1.55 | 1.61 | 81.6 | 0.418 | 2.2 | 3.1 | 3603 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 1.55 | 30 | 57244 | 3060 | 98.37 | 0.19518 | 0.19355 | 0.22577 | RANDOM | 24.107 |
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] | |
-0.13 | 0.86 | -0.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.099 |
r_dihedral_angle_4_deg | 14.175 |
r_dihedral_angle_3_deg | 12.167 |
r_dihedral_angle_1_deg | 6.019 |
r_scangle_it | 2.976 |
r_scbond_it | 1.892 |
r_angle_refined_deg | 1.361 |
r_mcangle_it | 1.078 |
r_mcbond_it | 0.707 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2833 |
Nucleic Acid Atoms | |
Solvent Atoms | 420 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345dtb | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SOLVE | phasing |