Joint X-ray/neutron structure of Trichoderma reesei xylanase II at pH 5.8
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 5.8 | 290 | PEG8000, 0.1M NaCacodylate, 0.2M NaI, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.5 | 50.9 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 49.514 | α = 90 |
b = 59.872 | β = 90 |
c = 70.431 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 290 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC VARIMAX | 2014-03-12 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 290 | IMAGE PLATE | MAATEL | | 2013-01-15 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
2 | | OTHER | 3.39 | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (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 |
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1 | 1.6 | 25.93 | 96.6 | 0.075 | | | | | | 8.5 | 3.7 | | 27489 | | | |
2 | 2 | 50 | 96.2 | 0.097 | | | | | | 11.2 | 4.7 | | 13899 | | 1.5 | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.6 | 1.66 | | 0.484 | | | | | | 1.5 | 3.6 | |
2 | 2 | 2.07 | | 0.327 | | | | | | 3.1 | 3.3 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.6 | 20 | | | 28272 | 24784 | 1239 | 87.7 | | | 0.196 | 0.205 | RANDOM | 36.81 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 20 | | | 14661 | 12917 | 619 | 88.1 | | | 0.164 | 0.182 | RANDOM | 36.81 |
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] |
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| | | | | |
| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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x_dihedral_angle_d | 16.6 |
x_dihedral_angle_d | 16.6 |
x_angle_deg | 1.2 |
x_angle_deg | 1.2 |
x_improper_angle_d | 1.14 |
x_improper_angle_d | 1.14 |
x_bond_d | 0.006 |
x_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1480 |
Nucleic Acid Atoms | |
Solvent Atoms | 148 |
Heterogen Atoms | 1 |
Software
Software |
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Software Name | Purpose |
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nCNS | refinement |
HKL-3000 | data collection |
DENZO | data reduction |
HKL-3000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |