5NFJ
Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277.15 | Well solution: 12% PEG 1000, 28% glycerol, 1.5%(w/v) PEG 3350 Cryo: 25% propylene glycol Protein concentration: 11 mg/mL |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.43 | 64.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 82.64 | α = 90 |
| b = 82.64 | β = 90 |
| c = 148.62 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 |
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 | 2015-10-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92820 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.96 | 82.64 | 99.98 | 0.052 | 0.999 | 16.95 | 6.9 | 67692 | |||||||||||
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 | THROUGHOUT | 1.96 | 82.64 | 67692 | 3570 | 99.98 | 0.18649 | 0.18533 | 0.20648 | RANDOM | 53.966 | |||||||
| 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] | |
| 1.37 | 1.37 | -2.74 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.296 |
| r_dihedral_angle_4_deg | 17.549 |
| r_dihedral_angle_3_deg | 13.894 |
| r_long_range_B_other | 9.916 |
| r_long_range_B_refined | 9.914 |
| r_scangle_other | 7.903 |
| r_dihedral_angle_1_deg | 6.993 |
| r_mcangle_it | 6.453 |
| r_mcangle_other | 6.452 |
| r_scbond_it | 5.495 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4387 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 217 |
| Heterogen Atoms | 139 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| SHELXD | phasing |
