6XT2
EQADH-NADH-HEPTAFLUOROBUTANOL, P21
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5VL0 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICRODIALYSIS | 7 | 278 | 10 mg/ml protein, 1 mM NAD+, 4 mM 1H,1H-heptafluorobutanol, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethananesulfonate, 10-25% 2-methyl-2,4-pentanediol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.24 | 48.12 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 50.15 | α = 90 |
| b = 180.27 | β = 105.83 |
| c = 86.9 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | AREA DETECTOR | RIGAKU | confocal | 2004-04-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.55 | 19.92 | 88.3 | 0.049 | 0.053 | 20.7 | 5.64 | 188871 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.55 | 1.61 | 77.2 | 0.279 | 0.346 | 3.1 | 2.62 | ||||||||||||
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 | 5VL0 | 1.55 | 19.84 | 187028 | 1769 | 88.26 | 0.1382 | 0.1377 | 0.1923 | RANDOM | 20.908 | ||||||
| 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] | |
| 1.29 | 0.06 | -0.97 | -0.31 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.655 |
| r_dihedral_angle_4_deg | 13.303 |
| r_dihedral_angle_3_deg | 12.6 |
| r_dihedral_angle_1_deg | 6.854 |
| r_rigid_bond_restr | 3.498 |
| r_angle_refined_deg | 1.977 |
| r_angle_other_deg | 1.504 |
| r_chiral_restr | 0.101 |
| r_bond_refined_d | 0.015 |
| r_gen_planes_refined | 0.011 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11140 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1238 |
| Heterogen Atoms | 296 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| d*TREK | data scaling |
| PDB_EXTRACT | data extraction |
| d*TREK | data reduction |
| REFMAC | phasing |
