Neutron structure of ferric ascorbate peroxidase
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, HANGING DROP | | 300 | Lithium Sulfate
HEPES |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.3 | 46.48 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 82.904 | α = 90 |
b = 82.904 | β = 90 |
c = 75.868 | γ = 90 |
Symmetry |
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Space Group | P 42 21 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 | 100 | IMAGE PLATE | MAATEL IMAGINE | | 2017-10-01 | L | LAUE |
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | | 2017-10-30 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.87-3.4 | ILL | LADI III |
2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 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 | 2.2 | 36.68 | 77.5 | 0.1 | | | | | | 5.9 | 3.3 | | 10136 | | | |
2 | 1.9 | 20.11 | 99.9 | 0.1 | | | | | | 11.1 | 11.2 | | 21444 | | | |
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 | 2.3 | | 0.2 | | | | | | | | |
2 | 1.9 | 1.94 | | 0.7 | | | | | | | | |
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 | 1.9 | 20.107 | | 1.36 | | 21404 | 1071 | 99.99 | | 0.1467 | 0.1445 | 0.1885 | | 31.17 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.222 | 37.076 | | 1.79 | | 10135 | 508 | 74.75 | | 0.278 | 0.2763 | 0.3076 | | |
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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-3.7555 | | | -3.7555 | | -5.7725 |
-3.7555 | | | -3.7555 | | -5.7725 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 13.938 |
f_angle_d | 1.521 |
f_chiral_restr | 0.092 |
f_bond_d | 0.013 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1905 |
Nucleic Acid Atoms | |
Solvent Atoms | 368 |
Heterogen Atoms | 78 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
PDB_EXTRACT | data extraction |