1W3M
Crystal structure of tsushimycin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 0.1 M NAAC/HAC PH=4.0 0.12 M HAC 38% ETOH 0.80 M CACL2 0.40 M 1,6-HEXANEDIOL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 40 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.488 | α = 65.64 |
b = 36.386 | β = 68.35 |
c = 37.511 | γ = 69.88 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | MARRESEARCH | MIRRORS | 2003-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 26.02 | 96.2 | 0.1 | 9.49 | 4.5 | 355145 |
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 | 1.1 | 92.1 | 0.5 | 3.35 | 3.62 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | DIRECT METHODS | FREE R-VALUE | 1 | 99 | 75901 | 3848 | 96.2 | 0.1385 | 0.1374 | 0.1711 | THIN 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 |
26 | 829 | 1259.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.428 |
s_non_zero_chiral_vol | 0.117 |
s_zero_chiral_vol | 0.09 |
s_approx_iso_adps | 0.089 |
s_similar_adp_cmpnt | 0.049 |
s_angle_d | 0.033 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist | |
s_anti_bump_dis_restr |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 924 |
Nucleic Acid Atoms | |
Solvent Atoms | 191 |
Heterogen Atoms | 161 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
XDS | data reduction |
XDS | data scaling |
SHELXD | phasing |