Neutron structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) low pH vapor exchange
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
---|
Type | Source | Accession Code | Details |
---|
|
experimental model | PDB | 5TKH | |
Crystallization
Crystalization Experiments |
---|
ID | Method | pH | Temperature | Details |
---|
1 | VAPOR DIFFUSION | 4.4 | 295 | PEG 3350, HEPES |
Crystal Properties |
---|
Matthews coefficient | Solvent content |
---|
2.16 | 42.98 |
Crystal Data
Unit Cell |
---|
Length ( Å ) | Angle ( ˚ ) |
---|
a = 68.296 | α = 90 |
b = 42.269 | β = 98.47 |
c = 70.413 | γ = 90 |
Symmetry |
---|
Space Group | P 1 21 1 |
---|
Diffraction
Diffraction Experiment |
---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
---|
1 | 1 | x-ray | 295 | PIXEL | DECTRIS EIGER R 4M | | 2018-10-25 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 295 | DIFFRACTOMETER | ORNL ANGER CAMERA | | 2018-07-17 | L | LAUE |
Radiation Source |
---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
---|
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 | | |
2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2-4 | ORNL Spallation Neutron Source | MANDI |
Data Collection
Overall |
---|
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 |
---|
1 | 1.9 | 12.65 | 97.56 | 0.1152 | | 0.1258 | | 0.991 | | 15.24 | 6.1 | | 30950 | | | 17.17 |
2 | 2.14 | 14.65 | 84.65 | 0.1532 | | 0.1751 | | 0.97 | | 10.01 | 4 | | 18963 | | | 17.17 |
Highest Resolution Shell |
---|
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) |
---|
1 | 1.9 | 1.9 | | 0.299 | | 0.3443 | | 0.88 | | 4.4 | 4.1 | |
2 | 2.14 | 2.22 | | 0.328 | | 0.3824 | | 0.363 | | 3.02 | 3.3 | |
Refinement
Statistics |
---|
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 |
---|
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 12.662 | | 1.34 | | 30948 | 1557 | 97.96 | | 0.1303 | 0.1275 | 0.182 | Random selection | 23.5275 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.144 | 14.649 | | | | 18770 | 954 | 84.98 | | 0.148 | 0.1444 | 0.2137 | Random selection | |
Temperature Factor Modeling |
---|
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 |
---|
Key | Refinement Restraint Deviation |
---|
f_dihedral_angle_d | 21.0533 |
f_angle_d | 1.3218 |
f_chiral_restr | 0.0707 |
f_bond_d | 0.0101 |
f_plane_restr | 0.0071 |
Non-Hydrogen Atoms Used in Refinement |
---|
Non-Hydrogen Atoms | Number |
---|
Protein Atoms | 3271 |
Nucleic Acid Atoms | |
Solvent Atoms | 1167 |
Heterogen Atoms | 155 |
Software
Software |
---|
Software Name | Purpose |
---|
PHENIX | refinement |
CrysalisPro | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
LaueView | data scaling |