2YGJ
Methanobactin MB4
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1 M HEPES PH 7.5, 4.3M NACL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.78 | 15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 9.06 | α = 90 |
b = 13.32 | β = 90 |
c = 42.65 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC CCD | 2011-02-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
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 | 0.8 | 14.22 | 78.3 | 0.06 | 23.1 | 7.6 | 4702 | 2 |
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 | 0.8 | 0.84 | 27.8 | 0.45 | 3.2 | 4.4 |
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 | SAD | FREE R-VALUE | NONE | 0.8 | 20 | 4446 | 210 | 79 | 0.087 | 0.0864 | 0.1091 | 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 |
3 | 35 | 73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.042 |
s_similar_adp_cmpnt | 0.015 |
s_bond_d | 0.008 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_angle_d | |
s_similar_dist | |
s_from_restr_planes | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol | |
s_anti_bump_dis_restr |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 59 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms | 3 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELXL-97 | refinement |
XDS | data reduction |
SCALA | data scaling |
SHELXCDE | phasing |