Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 Angstrom from unknown human gut bacteria (Uhgb_MP)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1VKD | PDB ENTRY 1VKD |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, pH 7.0 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.22 | 44.66 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 84.116 | α = 90 |
| b = 141.206 | β = 90 |
| c = 176.245 | 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 | 100 | PIXEL | DECTRIS PIXEL | MIRRORS | 2014-02-21 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.8 | 48 | 98.1 | 0.09 | 10.46 | 4.9 | 190253 | -1 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.8 | 1.91 | 88.7 | 0.7 | 1.63 | 3.7 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | 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 | THROUGHOUT | PDB ENTRY 1VKD | 1.8 | 110.2 | 180598 | 9557 | 98.05 | 0.1571 | 0.15537 | 0.17 | 0.18993 | 0.2 | RANDOM | 34.765 | ||||
| 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] | |
| -0.44 | 0.13 | 0.3 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 26.752 |
| r_dihedral_angle_4_deg | 15.614 |
| r_dihedral_angle_3_deg | 13.353 |
| r_dihedral_angle_1_deg | 6.858 |
| r_scbond_it | 2.092 |
| r_mcangle_it | 2.043 |
| r_angle_refined_deg | 1.922 |
| r_mcbond_it | 1.375 |
| r_mcbond_other | 1.375 |
| r_angle_other_deg | 0.913 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15371 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1063 |
| Heterogen Atoms | 312 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
