Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 2GUB | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 5.9 | 280 | crystals grew with ammonium sulfate as a precipitant at pH of 5.9, batch crystallization, temperature 280K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.78 | 55.76 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 93.908 | α = 90 |
b = 99.503 | β = 90 |
c = 102.971 | 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 | | 2010-09-15 | L | TOF LAUE |
2 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2010-06-14 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | NUCLEAR REACTOR | LANSCE BEAMLINE PCS | 0.6-7.0 | LANSCE | PCS |
2 | ROTATING ANODE | RIGAKU FR-E+ DW | 1.5418 | | |
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 | 28.46 | 86.9 | 0.225 | | | | | | 4.5 | 3 | 28290 | 28290 | 2.2 | 1.5 | |
2 | 1.7 | 29.86 | 99.2 | 0.077 | | | | | | 8.6 | 3.222 | 53087 | 53087 | | | |
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 | 2.11 | | 0.385 | 0.385 | | | | | 1.3 | 1.7 | |
2 | 1.7 | 1.76 | | 0.315 | 0.315 | | | | | 2.6 | 2.88 | |
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 | 2 | 20 | | 2.2 | 28290 | 26760 | 1347 | 81.4 | | 0.254 | 0.254 | 0.28 | RANDOM | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.7 | 20 | | 2.5 | | 49805 | 2507 | 93.6 | | 0.254 | 0.195 | 0.211 | 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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x_dihedral_angle_d | 17.9 |
x_dihedral_angle_d | 17.9 |
x_angle_deg | 1 |
x_angle_deg | 1 |
x_improper_angle_d | 0.82 |
x_improper_angle_d | 0.82 |
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 | 3054 |
Nucleic Acid Atoms | |
Solvent Atoms | 264 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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nCNS | refinement |
d*TREK | data scaling |
d*TREK | data reduction |
LAUENORM | data reduction |
LAUENORM | data scaling |