Neurospora crassa polysaccharide monooxygenase 2 resting state joint X-ray/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 | 4EIR | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION | 6 | 295 | PEG 3350, HEPES |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.15 | 42.7 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 68.12 | α = 90 |
b = 42.23 | β = 98.33 |
c = 70.29 | γ = 90 |
Symmetry |
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Space Group | P 1 21 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++ | | 2016-09-13 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 298 | IMAGE PLATE | MAATEL IMAGINE | | 2016-03-18 | 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 | 1.542 | | |
2 | NUCLEAR REACTOR | ORNL High Flux Isotope Reactor BEAMLINE CG4D | 2.85,4.5 | ORNL High Flux Isotope Reactor | CG4D |
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 | 1.5 | 36.1 | 91.6 | 0.054 | | 0.063 | 0.033 | 0.994 | | 13.8 | 3.8 | | 58482 | | | 16.04 |
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 | 1.5 | 1.53 | | 0.39 | | 0.454 | 0.232 | 0.855 | | | 3.8 | 2692 |
1 | 8.22 | 36.1 | | 0.03 | | 0.036 | 0.019 | 0.994 | | | 3.3 | 425 |
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 | 1.5 | 36.097 | | | | 57483 | 1967 | 90.19 | | 0.1486 | 0.1475 | 0.1785 | | |
NEUTRON DIFFRACTION | | 2.115 | 32.866 | | | | 18134 | 630 | 79.02 | | 0.2172 | 0.2159 | 0.2525 | | |
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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f_dihedral_angle_d | 21.28 |
f_dihedral_angle_d | 21.28 |
f_angle_d | 1.753 |
f_angle_d | 1.753 |
f_chiral_restr | 0.076 |
f_chiral_restr | 0.076 |
f_plane_restr | 0.014 |
f_plane_restr | 0.014 |
f_bond_d | 0.011 |
f_bond_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 3272 |
Nucleic Acid Atoms | |
Solvent Atoms | 382 |
Heterogen Atoms | 58 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
LAUEGEN | data reduction |
LSCALE | data scaling |
SCALA | data scaling |
PHASER | phasing |