3C3P
Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 10.3 | 277 | NANODROP, 0.2M Sodium chloride, 18.0% PEG 8000, 0.1M CAPS pH 10.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP | 10.5 | 277 | NANODROP, 0.2M Sodium chloride, 20.0% PEG 8000, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 156.88 | α = 90 |
b = 76.044 | β = 118.27 |
c = 85.173 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-11-20 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2007-10-25 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 1.00000 | SSRL | BL11-1 |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97939, 0.97953, 0.91840 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||
1,2 | 1.9 | 28.318 | 99.9 | 0.056 | 0.056 | 7.8 | 3.8 | 69499 | 35.05 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
1,2 | 1.9 | 1.95 | 100 | 0.507 | 0.507 | 1.3 | 3.8 | 5126 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MAD | THROUGHOUT | 1.9 | 28.318 | 69497 | 3515 | 99.87 | 0.201 | 0.199 | 0.232 | RANDOM | 29.203 |
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] | |
-0.41 | 0.24 | -0.3 | 0.93 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.787 |
r_dihedral_angle_3_deg | 11.803 |
r_dihedral_angle_4_deg | 11.485 |
r_dihedral_angle_1_deg | 2.457 |
r_scangle_it | 1.918 |
r_angle_refined_deg | 1.867 |
r_mcangle_it | 1.805 |
r_angle_other_deg | 1.496 |
r_scbond_it | 1.273 |
r_mcbond_it | 1.097 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4466 |
Nucleic Acid Atoms | |
Solvent Atoms | 195 |
Heterogen Atoms | 161 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SOLVE | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |