5EBA
Crystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F8Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 8.5 | 293 | 0.1M NaCl, 150mM MgCl2, 0.1M Tris-HCl pH 8.5, 15% PEG 6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.86 | α = 90 |
b = 80.11 | β = 111.19 |
c = 69.21 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | IMAGE PLATE | MAR scanner 345 mm plate | 2010-09-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.3 | 64.531 | 91.9 | 0.059 | 0.069 | 0.034 | 14.3 | 3.8 | 15361 | 15361 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.3 | 2.42 | 93.8 | 0.218 | 0.218 | 0.13 | 3.5 | 3.6 | 2271 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2f8q | 2.3 | 64.53 | 14620 | 732 | 91.42 | 0.1807 | 0.178 | 0.2349 | RANDOM | 32.416 |
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] | |
-1.66 | -0.91 | 1.28 | 0.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.769 |
r_dihedral_angle_3_deg | 13.452 |
r_dihedral_angle_4_deg | 13.302 |
r_dihedral_angle_1_deg | 5.899 |
r_mcangle_it | 1.297 |
r_angle_refined_deg | 1.095 |
r_angle_other_deg | 0.753 |
r_mcbond_other | 0.747 |
r_mcbond_it | 0.746 |
r_chiral_restr | 0.063 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2888 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SCALA | data reduction |
PHASER | phasing |