3RU2
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADPH.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2AX3 | PDB ENTRY 2AX3 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.63 | 53.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 122.29 | ¦Á = 90 |
| b = 122.29 | ¦Â = 90 |
| c = 155.779 | ¦Ã = 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 | CCD | ADSC QUANTUM 315 | MIRRORS | 2009-06-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97857 | APS | 19-ID |
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 | 50 | 99.8 | 0.135 | 0.135 | 23.626 | 8.9 | 30530 | 30203 | -3 | |||||||||
| 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 | 2.24 | 98.2 | 0.677 | 0.677 | 1.772 | 6.2 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2AX3 | 2.2 | 50 | 28561 | 1515 | 99.34 | 0.1638 | 0.16153 | 0.20642 | RANDOM | 31.85 | ||||||
| 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] | |
| -1.2 | -1.2 | 2.39 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.826 |
| r_dihedral_angle_3_deg | 15.266 |
| r_dihedral_angle_4_deg | 14.188 |
| r_dihedral_angle_1_deg | 6.256 |
| r_scangle_it | 5.086 |
| r_angle_other_deg | 4.179 |
| r_scbond_it | 3.097 |
| r_angle_refined_deg | 1.853 |
| r_mcangle_it | 1.794 |
| r_mcbond_it | 0.942 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3773 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 97 |
| Heterogen Atoms | 90 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
