3EU3
Crystal Structure of BdbD from Bacillus subtilis (reduced)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 27% PEG2000, 0.1M ammonium acetate, 0.1M MES, pH6.5, 1mM DTT,cryo-protected with 20% Ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.774 | α = 90 |
b = 43.399 | β = 107.4 |
c = 54.658 | 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 | 100 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.5 | 28.21 | 97.8 | 0.052 | 15 | 3.5 | 27450 | 27450 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.5 | 1.58 | 89.5 | 0.267 | 3.4 | 2.9 | 27450 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | THROUGHOUT | 1.5 | 26.08 | 26211 | 26211 | 1385 | 98.83 | 0.18776 | 0.18608 | 0.18 | 0.21919 | 0.22 | RANDOM | 18.639 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
0.26 | -0.05 | 0.9 | -1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.327 |
r_dihedral_angle_3_deg | 14.006 |
r_dihedral_angle_1_deg | 5.251 |
r_sphericity_free | 4.729 |
r_sphericity_bonded | 3.612 |
r_scangle_it | 3.286 |
r_scbond_it | 2.211 |
r_dihedral_angle_4_deg | 1.856 |
r_mcangle_it | 1.605 |
r_rigid_bond_restr | 1.361 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1538 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
BP3 | model building |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
BP3 | phasing |