1KQP
NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1EE1 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | microgravity/vapor diffusion | 8.5 | 298 | 25% PEG 400, 0.05M Tris, 0.05M MgCl2, 0.005M NaAD, 0.0025M ATP, pH 8.5, microgravity/vapor diffusion at 298K, microgravity/vapor diffusion |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.97 | 36 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.28 | α = 90 |
| b = 84.79 | β = 110.5 |
| c = 59.64 | 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 | 120 | IMAGE PLATE | MARRESEARCH | 1998-08-01 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.9050 | EMBL/DESY, HAMBURG | X11 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.028 | 30 | 96.7 | 0.048 | 32.8 | 3.4 | 239033 | 231200 | -1 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.028 | 1.08 | 72.3 | 0.381 | 2.4 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R | 1EE1 | 1.03 | 10 | 4 | 216026 | 179414 | 10811 | 83 | 0.1077 | 0.1063 | 0.1063 | 0.1354 | RANDOM | |||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 18 | 4272.09 | 5072.19 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_anti_bump_dis_restr | 0.149 |
| s_non_zero_chiral_vol | 0.089 |
| s_zero_chiral_vol | 0.083 |
| s_approx_iso_adps | 0.068 |
| s_similar_adp_cmpnt | 0.039 |
| s_angle_d | 0.031 |
| s_from_restr_planes | 0.0282 |
| s_bond_d | 0.015 |
| s_rigid_bond_adp_cmpnt | 0.007 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4264 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 714 |
| Heterogen Atoms | 195 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| SHELXL-97 | refinement |
