Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex, H2O solvent
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5XCY | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | COUNTER-DIFFUSION | 5.5 | 293 | polyethylene glycol 4000, sodium chloride, cellotriose, acetate buffer, |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.18 | 43.69 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 54.81 | α = 90 |
| b = 68.29 | β = 90 |
| c = 89.73 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | PIXEL | DECTRIS PILATUS 6M | | 2019-02-26 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 288 | DIFFRACTOMETER | iBIX | | 2019-02-01 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1 | Photon Factory | BL-5A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.9-5.6 | JPARC MLF | BL-03 |
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 | 1.8 | 50 | 100 | 0.087 | | | | | | 19.3 | 6.5 | | 31948 | | | 14.99 |
| 2 | 2.59 | 20.29 | 89.5 | 0.294 | | | | | | 6.3 | 2.6 | | 9816 | | | |
| 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 | 1.8 | 1.83 | | 0.254 | | | | | | | | |
| 2 | 2.59 | 2.69 | | 0.623 | | | | | | | | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.8 | 46.73 | | 1.39 | | 31885 | 1616 | 99.74 | | 0.1324 | 0.1313 | 0.1332 | 0.1534 | 0.1556 | | 16.55 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.59 | 20.29 | | | | 9808 | | 89.5 | | | 0.2224 | | 0.2419 | | | |
| 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 | 14.0194 |
| f_angle_d | 0.9619 |
| f_chiral_restr | 0.0598 |
| f_bond_d | 0.0108 |
| f_plane_restr | 0.0082 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2710 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 269 |
| Heterogen Atoms | 36 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | phasing |
| PHENIX | refinement |
| STARGazer | data reduction |
