6OWM
Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICRODIALYSIS | 7 | 298 | 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethane sulfonate, 0.25 mM EDTA, pH 6.7 at 25 deg C, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 14 to 25 % 2-methyl-2,4-pentanediol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.41 | 48.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.47 | α = 92.09 |
| b = 51.44 | β = 102.95 |
| c = 92.56 | γ = 110.25 |
| Symmetry | |
|---|---|
| Space Group | P 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 | CCD | MARMOSAIC 300 mm CCD | adjustable foculs K-B pari SiPlus PT, RH coatings | 2007-06-16 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.0332 | APS | 23-ID-B |
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 | 1.1 | 19.62 | 88.6 | 0.075 | 0.082 | 11.4 | 5.15 | 267734 | |||||||||||
| 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 | 1.1 | 1.14 | 56.8 | 0.28 | 0.329 | 3.1 | 3.44 | ||||||||||||
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 | 6o91 | 1.1 | 19.62 | 265082 | 2622 | 88.55 | 0.12402 | 0.12386 | 0.14059 | RANDOM | 15.811 | ||||||
| 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] | |
| 0.14 | -0.54 | 0.31 | 0.46 | 0.12 | -0.48 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.794 |
| r_dihedral_angle_1_deg | 17.844 |
| r_dihedral_angle_4_deg | 13.531 |
| r_dihedral_angle_3_deg | 10.888 |
| r_long_range_B_refined | 2.589 |
| r_rigid_bond_restr | 2.481 |
| r_long_range_B_other | 2.165 |
| r_scangle_other | 1.945 |
| r_angle_refined_deg | 1.843 |
| r_scbond_it | 1.676 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5576 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1024 |
| Heterogen Atoms | 142 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| d*TREK | data scaling |
| PDB_EXTRACT | data extraction |
| REFMAC | phasing |
| O | model building |
| d*TREK | data reduction |
