Room temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | | 7.7 | 293 | 50MM HEPES, 40% v/v (NH4)2SO4 (sat.), protein 40 MG/ML, PH 7.7, BATCH METHOD, temperature 293K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.77 | 55.59 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 94.04 | α = 90 |
b = 99.52 | β = 90 |
c = 102.47 | γ = 90 |
Symmetry |
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Space Group | I 2 2 2 |
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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 | neutron | 293 | AREA DETECTOR | POSITION-SENSITIVE HE3 NEUTRON DETECTOR | | 2009-04-15 | M | SINGLE WAVELENGTH |
2 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2009-02-15 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | NUCLEAR REACTOR | | 2.422 | | D19 |
2 | ROTATING ANODE | | 1.54 | | |
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 | 1.8 | 20 | 75 | | | | | | | | | 39080 | 29152 | 2.5 | 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 | 1.8 | 1.9 | | | | | | | | | | |
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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NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.8 | 20 | | 2.5 | 39080 | 29152 | 1209 | | | | 0.173 | 0.181 | RANDOM | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 20 | | 2.5 | | | 1546 | | | | 0.179 | 0.187 | RANDOM | |
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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c_angle_deg | 0.946 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 3054 |
Nucleic Acid Atoms | |
Solvent Atoms | 238 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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nCNS | refinement |
RETREAT | data reduction |
RETREAT | data scaling |
nCNS | phasing |