2AVN
CRYSTAL STRUCTURE OF A UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE-RELATED PROTEIN (TM1389) FROM THERMOTOGA MARITIMA MSB8 AT 2.35 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 5 | 293 | 1.0M LiCl, 10.0% PEG-600, 0.1M Citrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 5.0 |
| 2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 7 | 293 | 40.0% MPD, 0.1M HEPES, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 7.0 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 130.475 | α = 90 |
| b = 130.475 | β = 90 |
| c = 192.926 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 64 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 | CCD | MARMOSAIC 325 mm CCD | 2005-07-04 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 315 | flat mirror | 2005-06-14 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97915 | SSRL | BL9-2 |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.979318, 0.918370 | SSRL | BL11-1 |
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 | 2.35 | 29.8 | 99.6 | 0.183 | 0.183 | 3.4 | 9.8 | 40826 | |||||||||||
| 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 | 2.35 | 2.41 | 95.3 | 0.981 | 0.981 | 0.7 | 5.6 | ||||||||||||
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.35 | 29.8 | 38735 | 2048 | 99.69 | 0.171 | 0.169 | 0.199 | RANDOM | 44.977 | |||||||
| 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] | |
| 1.91 | 0.96 | 1.91 | -2.87 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.13 |
| r_dihedral_angle_4_deg | 16.095 |
| r_dihedral_angle_3_deg | 15.282 |
| r_scangle_it | 7.3 |
| r_dihedral_angle_1_deg | 6.452 |
| r_scbond_it | 5.32 |
| r_mcangle_it | 2.972 |
| r_mcbond_it | 2.165 |
| r_angle_refined_deg | 1.459 |
| r_angle_other_deg | 0.8 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3991 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 210 |
| Heterogen Atoms | 57 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| CCP4 | data scaling |
