Joint X-ray/neutron structure of Trichoderma reesei xylanase II at pH 4.4
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 | 4.4 | 290 | PEG8000, 0.1M NaOAc, 0.2M NaI, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.52 | 51.24 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 49.963 | α = 90 |
b = 59.621 | β = 90 |
c = 70.588 | 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 | 291 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC VARIMAX | 2014-03-12 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 291 | AREA DETECTOR | ANGER CAMERA/ORNL | | 2014-04-14 | L | LAUE |
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 | NUCLEAR REACTOR | ORNL Spallation Neutron Source BEAMLINE MANDI | 2-4 | ORNL Spallation Neutron Source | MANDI |
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 | 1.7 | 40 | 95.1 | 0.027 | | | | | | 39.8 | 4 | | 22796 | | | |
2 | 2 | 50 | 90.6 | 0.253 | | | | | | 6.2 | 4.8 | | 13899 | | 1.6 | |
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 | 1.7 | 1.76 | | 0.343 | | | | | | 2.7 | 4 | |
2 | 2 | 2.11 | | 0.271 | | | | | | 3.2 | 2.7 | |
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 | 1.7 | 29.81 | | | 23829 | 19008 | 951 | 79.8 | | | 0.199 | 0.211 | RANDOM | 28.71 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 9.89 | | | 14645 | 13048 | 636 | 89.1 | | | 0.261 | 0.304 | RANDOM | 28.71 |
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 | 15.7 |
x_dihedral_angle_d | 15.7 |
x_improper_angle_d | 2.01 |
x_improper_angle_d | 2.01 |
x_angle_deg | 1.2 |
x_angle_deg | 1.2 |
x_bond_d | 0.007 |
x_bond_d | 0.007 |
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 | 146 |
Heterogen Atoms | 1 |
Software
Software |
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Software Name | Purpose |
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nCNS | refinement |
HKL-3000 | data collection |
Mantid | data reduction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
CNS | phasing |