1ALX
GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GMA | PDB ENTRY 1GMA |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
1.65 | 25.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 14.907 | α = 90 |
b = 26.014 | β = 92.03 |
c = 31.911 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 1990-01-21 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |
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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 | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 284 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | model building |
SHELXL-97 | refinement |
ENRAF-NONIUS | data reduction |
SHELXL-97 | phasing |