Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature
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 | VAPOR DIFFUSION, SITTING DROP | | 293 | polyethylene glycol 3350, sodium chloride,2-methyl-2,4-pentandiol, acetate buffer |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.22 | 44.55 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 55.58 | α = 90 |
| b = 68.04 | β = 90 |
| c = 90.06 | 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 | | 2018-05-23 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 298 | DIFFRACTOMETER | iBIX | | 2018-04-27 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0 | 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 |
|---|
| 2 | 1.36 | 50 | 95.6 | 0.066 | | | | | | 32.2 | 10.5 | | 70839 | | | 13.85 |
| 1 | 1.86 | 21.5 | 94.2 | 0.336 | | | | | | 4.9 | 5.5 | | 27502 | | | 13.85 |
| 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) |
|---|
| 2 | 1.36 | 1.38 | | 0.286 | | | | | | | | |
| 1 | 1.86 | 1.94 | | 0.677 | | | | | | | | |
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 | 1.36 | 34.99 | | 1.39 | | 70782 | 3562 | 95.9 | | 0.1397 | 0.1389 | 0.1385 | 0.1561 | 0.1551 | | 20.8 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.86 | 21.5 | | | | 26666 | | 90.72 | | | 0.209 | | 0.232 | | | |
| 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 | 14.3966 |
| f_angle_d | 1.0401 |
| f_chiral_restr | 0.0829 |
| f_bond_d | 0.0111 |
| f_plane_restr | 0.0084 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2710 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 250 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| STARGazer | data reduction |
| PHENIX | phasing |
