5LAA
X-RAY STRUCTURE OF THE METHYLTRANSFERASE SUBUNIT A FROM METHANOTHERMUS FERVIDUS IN COMPLEX WITH COBALAMIN
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 298 | Protein concentration 20 mg/mL complexed with hydroxy-cobalamin. A pink brick shape crystal appeared in 26% PEG 3000, 100 mM Na citrate pH 5.5. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.05 | 59.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 100.604 | α = 90 |
| b = 100.604 | β = 90 |
| c = 262.706 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2014-07-27 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.602 | SLS | X10SA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | CC (Half) | 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 | 3 | 131.35 | 98.5 | 0.224 | 0.074 | 0.995 | 8.6 | 17.1 | 13764 | ||||||||||
| 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 | 3 | 3.18 | 91 | 1.06 | 2.5 | 11.9 | |||||||||||||
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 | SAD | FREE R-VALUE | 3 | 131.35 | 13073 | 681 | 98.31 | 0.21057 | 0.20838 | 0.25424 | RANDOM | 86.158 | |||||||
| 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] | |
| 4.35 | 4.35 | -8.69 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.383 |
| r_dihedral_angle_3_deg | 18.251 |
| r_dihedral_angle_4_deg | 17.208 |
| r_dihedral_angle_1_deg | 6.406 |
| r_long_range_B_refined | 5.786 |
| r_long_range_B_other | 5.785 |
| r_scangle_other | 3.432 |
| r_mcangle_it | 3.306 |
| r_mcangle_other | 3.306 |
| r_angle_refined_deg | 2.302 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3644 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 273 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| AutoSol | phasing |
