4QDM
Crystal structure of N-terminal mutant (V1L) 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 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 0.1M NaCl, 0.16M MgCl2, 0.05M Tris HCl pH 8.5, 18% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.88 | α = 90 |
b = 76.58 | β = 90 |
c = 176.73 | 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 | MARMOSAIC 225 mm CCD | MIRRORS | 2012-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.82656 | ESRF | BM14 |
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 | 1.964 | 88.365 | 97.3 | 0.076 | 18.5 | 6.9 | 52548 | 52548 |
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 | 1.96 | 2.07 | 94.3 | 0.213 | 0.213 | 0.088 | 3.5 | 6.6 | 7277 |
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 | 1.964 | 40.19 | 52480 | 2682 | 97.1 | 0.1535 | 0.1516 | 0.1901 | RANDOM | 14.558 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.38 | -0.35 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.734 |
r_dihedral_angle_4_deg | 14.392 |
r_dihedral_angle_3_deg | 11.447 |
r_dihedral_angle_1_deg | 6.152 |
r_angle_other_deg | 1.986 |
r_angle_refined_deg | 1.802 |
r_mcangle_it | 1.404 |
r_mcbond_it | 0.867 |
r_mcbond_other | 0.867 |
r_chiral_restr | 0.122 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5792 |
Nucleic Acid Atoms | |
Solvent Atoms | 434 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
PHASER | phasing |