1F0L
1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 2 MICROLITERS OF PROTEIN SOLUTION CONSISTING OF: 8 MG/ML WILD TYPE DIPHTHERIA TOXIN MONOMER + APUP, 0.5 MILLIMOLAR EDTA, 50 MILLIMOLAR TRIS-HCL, PH 7.5 PLUS 2 MICROLITERS OF RESERVIOR SOLUTION CONSISTING OF: 17% PEG 8000, 1 MOLAR SODIUM CHLORIDE, 50 MILLIMOLAR TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 38.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 167.77 | α = 90 |
| b = 134.88 | β = 90 |
| c = 46.87 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
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 4 | 1997-11-09 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X12B | NSLS | X12B | |
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 | 1.55 | 40 | 97 | 0.057 | 6.8 | 3.9 | 583084 | 149412 | 20.1 | ||||||||||
| 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) | |||||||||||
| 1.55 | 1.62 | 81.5 | 0.285 | 2.5 | 2.8 | 18092 | |||||||||||||
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 | FREE R | 1MDT | 1.55 | 40 | 149412 | 149412 | 7212 | 97 | 0.188 | 0.188 | 0.188 | 0.238 | NCS-RELATED (G.PFLUEGL) | |||||
| 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 |
| 78 | 7782 | 9442 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_non_zero_chiral_vol | 0.045 |
| s_zero_chiral_vol | 0.044 |
| s_anti_bump_dis_restr | 0.039 |
| s_similar_adp_cmpnt | 0.031 |
| s_from_restr_planes | 0.0256 |
| s_angle_d | 0.023 |
| s_bond_d | 0.008 |
| s_similar_dist | |
| s_rigid_bond_adp_cmpnt | |
| s_approx_iso_adps | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8300 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1809 |
| Heterogen Atoms | 95 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHELXL | refinement |
| SHELXL-97 | refinement |
| CCP4 | data scaling |
