Engineered CBM X-2 L110F in complex with branched carbohydrate XXXG.
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4BJ0 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | Large crystals were grown in 9-well glass plates using Hampton sandwich box set-up. |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.3 | 46.59 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 72.977 | α = 90 |
| b = 49.856 | β = 90 |
| c = 45.091 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 2 | 1 | neutron | 293 | IMAGE PLATE | FUJI | | 2014-11-25 | M | SINGLE WAVELENGTH |
| 1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | | 2014-10-28 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 2.66 | FRM II | BIODIFF |
| 1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | 1.04 | MAX II | I911-2 |
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 | 1.6 | 45 | 91.1 | 0.041 | | | | | | 6.6 | 3 | | 20530 | | | |
| 1 | 1.6 | 29.3 | 97.7 | 0.093 | | | | | | 28.6 | 5.5 | | 21610 | | | |
| 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 | 1.6 | 1.7 | | 0.231 | | | | | | 7.8 | 5.5 | 3389 |
| 2 | 1.6 | 1.65 | | 0.449 | | | | | | 1.8 | 2.5 | 1485 |
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 | 1.6 | 45 | | | | 20512 | 1027 | 91.09 | | 0.2239 | 0.2225 | 0.17 | 0.25 | 0.21 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.606 | 29.445 | | | | 21609 | 1081 | 97.69 | | 0.1648 | 0.1628 | | 0.204 | | | |
| 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 | 22.277 |
| f_dihedral_angle_d | 22.277 |
| f_angle_d | 1.268 |
| f_angle_d | 1.268 |
| f_chiral_restr | 0.08 |
| f_chiral_restr | 0.08 |
| f_bond_d | 0.01 |
| f_bond_d | 0.01 |
| f_plane_restr | 0.006 |
| f_plane_restr | 0.006 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1260 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 60 |
| Heterogen Atoms | 73 |
| Protein Atoms | 1260 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 60 |
| Heterogen Atoms | 73 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| Coot | model building |
