2Q8X
The high-resolution crystal structure of ixt6, a thermophilic, intracellular xylanase from G. stearothermophilus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1R85 | 1R85 Initial model of Xylanase T-6 (family10) of G.bacillus stearothermophilus |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 1.9M sodium acetate, 0.1M cacodylate pH=6.5, 293.0 K, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.48 | 64.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 169.481 | α = 90 |
b = 80.579 | β = 91.89 |
c = 79.054 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 4 | 2001-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X26C | 1.1 | NSLS | X26C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.45 | 38 | 91.6 | 0.058 | 18.1 | 7 | 187710 | 171850 | 18.1 | 22.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.45 | 1.48 | 52.3 | 0.444 | 0.342 | 1.5 | 5.5 |
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 | MOLECULAR REPLACEMENT | FREE R | 1R85 Initial model of Xylanase T-6 (family10) of G.bacillus stearothermophilus | 1.45 | 15 | 156685 | 6741 | 83.5 | 0.15 | 0.1499 | 0.1901 | RANDOM | 30.434 |
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 |
29 | 6135.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.101 |
s_non_zero_chiral_vol | 0.073 |
s_zero_chiral_vol | 0.059 |
s_similar_adp_cmpnt | 0.037 |
s_angle_d | 0.03 |
s_from_restr_planes | 0.029 |
s_anti_bump_dis_restr | 0.02 |
s_bond_d | 0.012 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5385 |
Nucleic Acid Atoms | |
Solvent Atoms | 679 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
SCALEPACK | data scaling |
CNS | refinement |
SHELX | refinement |
PDB_EXTRACT | data extraction |
CNS | phasing |
DENZO | data reduction |