Neutron crystal structure of wtT4LE
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 5VNQ | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.78 | 55.77 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 60.87 | α = 90 |
b = 60.87 | β = 90 |
c = 96.87 | γ = 120 |
Symmetry |
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Space Group | P 32 2 1 |
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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 | 298 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2017-08-01 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 298 | IMAGE PLATE | ORNL ANGER CAMERA | | 2017-08-01 | 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 | 1.5418 | | |
2 | NUCLEAR REACTOR | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.0-4.0 | 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 | 2 | 45 | 96.6 | 0.09 | | | | | | 8.7 | 2.1 | | 14086 | | | 27.14 |
2 | 2.1 | 15 | 86.2 | 0.129 | | | | | | 7.2 | 4.9 | | 10605 | | | 27.14 |
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 | 2 | 2.07 | | 0.475 | | | | | | 1.8 | | |
2 | 2.1 | 2.21 | | 0.192 | | | | | | 4.1 | | |
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 | 2 | 45 | | 1.34 | | 14086 | 627 | 96.63 | | 0.1672 | 0.1653 | 0.2015 | | 35.4003 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.1 | 15 | | | | 10605 | 542 | 84.41 | | 0.2197 | 0.2181 | 0.2496 | | |
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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Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1309 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms | 1 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
PDB_EXTRACT | data extraction |
Mantid | data reduction |
LaueView | data scaling |
PHASER | phasing |