8G4V
Horse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICRODIALYSIS | 7 | 278 | 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ~13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.28 | 46 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.17 | α = 92.02 |
| b = 51.59 | β = 102.89 |
| c = 92.77 | γ = 110.04 |
| 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 | ADSC QUANTUM 210 | 2004-07-24 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.000 | APS | 17-ID |
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 | 1.2 | 19.96 | 91.1 | 0.06 | 0.065 | 13.3 | 6.13 | 211946 | |||||||||||
| 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 | 1.2 | 1.24 | 74.4 | 0.181 | 0.212 | 3.5 | |||||||||||||
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 | 4dwv | 1.2 | 19.96 | 207414 | 2091 | 89.98 | 0.13518 | 0.13493 | 0.1607 | RANDOM | 17.445 | ||||||
| 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] | |
| 0.19 | -0.33 | 0.06 | 0.53 | 0.11 | -0.61 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.392 |
| r_dihedral_angle_4_deg | 13.729 |
| r_dihedral_angle_3_deg | 12.183 |
| r_dihedral_angle_1_deg | 6.595 |
| r_rigid_bond_restr | 4.988 |
| r_scangle_other | 3.215 |
| r_scbond_it | 3.139 |
| r_scbond_other | 3.139 |
| r_long_range_B_refined | 2.968 |
| r_long_range_B_other | 2.85 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5568 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 673 |
| Heterogen Atoms | 126 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data scaling |
| REFMAC | refinement |
| d*TREK | data reduction |
| O | model building |
