1N92
Horse Liver Alcohol Dehydrogenase Complexed with NAD+ and 4-Iodopyrazole
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1HLD | PDB ENTRY 1HLD |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | Dialysis | 7 | 277 | MPD, pH 7.0, Dialysis, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.17 | 42.89 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.2 | α = 78.96 |
| b = 51.05 | β = 75.47 |
| c = 93.23 | γ = 70.24 |
| 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 | IMAGE PLATE | RIGAKU RAXIS IV | confocal osmic | 2001-03-28 | 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) | 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 | 1.47 | 20 | 88.8 | 0.054 | 0.054 | 5.9 | 2.1 | 156075 | 109109 | ||||||||||
| 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) | ||||||||||
| 1.47 | 1.508 | 69 | 0.127 | 0.127 | 4.1 | 5097 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1HLD | 1.47 | 20 | 156075 | 109109 | 2234 | 88.8 | 0.1515 | 0.151 | 0.151 | 0.1831 | RANDOM | 17.152 | ||||
| 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] | |
| -0.25 | -0.02 | 0.78 | -0.21 | 0.04 | 0.06 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 9.496 |
| r_sphericity_bonded | 7.943 |
| r_dihedral_angle_1_deg | 6.051 |
| r_scangle_it | 5.258 |
| r_angle_other_deg | 3.608 |
| r_scbond_it | 3.604 |
| r_mcangle_it | 2.276 |
| r_angle_refined_deg | 1.634 |
| r_mcbond_it | 1.513 |
| r_rigid_bond_restr | 1.376 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5570 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 589 |
| Heterogen Atoms | 104 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data scaling |
| d*TREK | data reduction |
| AMoRE | phasing |
| REFMAC | refinement |
