Crystal structure of xylose isomerase from Piromyces E2 in complex with two Mg2+ ions and xylose
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5NH5 | D_1200004044 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 294 | 13-15 % PEG3350, 10 mM MgCl2, 0.1 M Hepes pH 7.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.3 | 45 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 78.6 | α = 115.4 |
| b = 79.28 | β = 89.91 |
| c = 91.969 | γ = 117.13 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | IMAGE PLATE | MARRESEARCH | 2014-11-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 39.5 | 92 | 0.093 | 0.089 | 0.985 | 6.1 | 2 | 125669 | 1.6 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.9 | 1.93 | 84.7 | 0.354 | 0.338 | 0.746 | 2 | 2 | |||||||||||
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 | D_1200004044 | 1.9 | 39.5 | 119324 | 6287 | 91.97 | 0.15381 | 0.15266 | 0.16 | 0.17572 | 0.18 | RANDOM | 15.51 | ||||
| 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] | |
| -0.05 | -0.03 | -0.02 | 0.03 | 0.01 | 0.02 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.743 |
| r_dihedral_angle_4_deg | 14.586 |
| r_dihedral_angle_3_deg | 13.258 |
| r_dihedral_angle_1_deg | 5.724 |
| r_long_range_B_refined | 5.049 |
| r_long_range_B_other | 4.577 |
| r_scangle_other | 1.63 |
| r_angle_refined_deg | 1.322 |
| r_scbond_it | 1.068 |
| r_mcangle_it | 1.021 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 13871 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1775 |
| Heterogen Atoms | 223 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
