1ALX
GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1GMA | PDB ENTRY 1GMA |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN METHANOL., PH 7.0, BATCH METHOD | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.65 | 25.57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 14.907 | α = 90 |
| b = 26.014 | β = 92.03 |
| c = 31.911 | 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 | DIFFRACTOMETER | ENRAF-NONIUS FAST | COLLIMATOR | 1990-01-09 | M | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RUH2R | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.25 | 100 | 99.9 | 85.41 | 1 | 7726 | -3 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.2 | 1.24 | 99 | 35.53 | 1 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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-VALUE | PDB ENTRY 1GMA | 1.2 | 100 | 7726 | 376 | 99.9 | 0.102 | 0.1 | 0.168 | 5% OF REFLECTIONS IN THIN RESOLUTION SHELLS. | |||||||
| 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 |
| 5 | 367.54 | 315.41 |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_from_restr_planes | 0.326 |
| s_zero_chiral_vol | 0.167 |
| s_non_zero_chiral_vol | 0.119 |
| s_approx_iso_adps | 0.045 |
| s_similar_adp_cmpnt | 0.033 |
| s_angle_d | 0.031 |
| s_bond_d | 0.014 |
| s_rigid_bond_adp_cmpnt | 0.006 |
| s_similar_dist | |
| s_anti_bump_dis_restr | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 284 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELXL-97 | model building |
| SHELXL-97 | refinement |
| ENRAF-NONIUS | data reduction |
| SHELXL-97 | phasing |
