7CD2
Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 293 | 25% PEG 4000, 0.45 M ammonium acetate, 0.1 M sodium acetate buffer pH 4.2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.984 | α = 90 |
b = 96.121 | β = 90 |
c = 263.314 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 95 | CCD | ADSC QUANTUM 270 | 2015-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0000 | Photon Factory | AR-NW12A |
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 | 2.7 | 150 | 93.3 | 0.115 | 15.5 | 11.8 | 62923 | 42.2 |
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 | 2.7 | 2.8 | 91.3 | 0.733 | 3.1 | 11.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5Y6U | 2.7 | 39.912 | 59674 | 3166 | 93.04 | 0.19046 | 0.18581 | 0.27701 | RANDOM | 54.087 |
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] | |
0.16 | -1.09 | 0.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.742 |
r_dihedral_angle_4_deg | 21.469 |
r_dihedral_angle_3_deg | 19.382 |
r_long_range_B_refined | 11.046 |
r_long_range_B_other | 11.046 |
r_scangle_other | 8.396 |
r_mcangle_it | 8.246 |
r_mcangle_other | 8.245 |
r_dihedral_angle_1_deg | 8.136 |
r_scbond_it | 5.668 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16838 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |