5VG1
Neutron crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase
NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5VG0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Purified enzyme was incubated with a threefold molar excess of CuSO4 for 30 min at room temperature. To remove excess copper, the protein was loaded onto a desalting column equilibrated with 20 mM Tris-HCl pH 8.0. 14 ul protein solution at 48 mg/ml was mixed with 14 ul reservoir buffer consisting of 1.9 M DL-malic acid pH 7.0 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.5 | α = 90 |
b = 76.4 | β = 90 |
c = 122.1 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | neutron | 295 | AREA DETECTOR | ORNL ANGER CAMERA | 2015-05-21 | L | LAUE |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | NUCLEAR REACTOR | ORNL Spallation Neutron Source BEAMLINE MANDI | 2-4 | ORNL Spallation Neutron Source | MANDI |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | |||||||||
1 | 2.1 | 12 | 76 | 9.4 | 4.5 | 13989 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.1 | 2.17 | 59.4 | 2.7 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5VG0 | 2.1 | 12 | 2.38 | 13989 | 686 | 76 | 0.191 | 0.187 | 0.265 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.89 |
f_angle_d | 0.56 |
f_chiral_restr | 0.04 |
f_bond_d | 0.002 |
f_plane_restr | 0.002 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | phasing |
Mantid | data reduction |