Crystal structure of human myelin protein P2 at room temperature from joint X-ray and neutron refinement.
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 | 2WUT | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, HANGING DROP | | 281 | 28% PEG 6000, 0.1 M citrate, pD 4.75 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.82 | 56.42 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 57.952 | α = 90 |
b = 57.952 | β = 90 |
c = 100.79 | γ = 90 |
Symmetry |
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Space Group | P 41 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 | 292 | AREA DETECTOR | LADI III | | 2014-09-02 | L | LAUE |
2 | 1 | x-ray | 293 | IMAGE PLATE | MAR scanner 345 mm plate | | 2016-05-02 | 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 | 3.0-3.9 | ILL | LADI III |
2 | SEALED TUBE | Xenocs GeniX 3D Cu 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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2 | 2 | 15 | 98.9 | | 0.06 | 0.063 | | 0.999 | | 25.2 | 9.7 | | 12464 | | | 27.66 |
1 | 2.4 | 40 | 60.1 | | 0.189 | | | | | 6.1 | 4.2 | | 4232 | | | 27.66 |
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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2 | 2 | 2.06 | | | 0.431 | 0.513 | | 0.849 | | 3 | 3.2 | |
1 | 2.4 | 2.53 | | | 0.304 | | | | | 2.8 | 2.2 | |
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 | 14.53 | | 1.34 | | 12443 | 1246 | 98.97 | | 0.1596 | 0.1546 | 0.2032 | | 18.85 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.4 | 40 | | | | 4227 | | 58.9 | | 0.2995 | 0.2947 | 0.3412 | | |
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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| | | | | |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 17.656 |
f_angle_d | 2.0852 |
f_chiral_restr | 0.104 |
f_bond_d | 0.0292 |
f_plane_restr | 0.0129 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1048 |
Nucleic Acid Atoms | |
Solvent Atoms | 105 |
Heterogen Atoms | 31 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |