6ITO
Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, AMP and inhibitor Ribose 5-Phosphate
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5WSC | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 277 | 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM AMP, 5 mM D-ribose 5-phosphate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.23 | 61.91 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 125.55 | α = 90 |
| b = 125.55 | β = 90 |
| c = 143.821 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 |
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 PILATUS 2M-F | 2016-09-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.00 | SLS | X06DA |
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 | 2.55 | 62.77 | 100 | 0.124 | 8.8 | 4 | 82657 | 38.9 | |||||||||||
| 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 | 2.55 | 2.6 | 100 | 0.94 | 1.6 | 4.1 | |||||||||||||
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 | 5WSC | 2.55 | 62.77 | 78503 | 4106 | 99.96 | 0.20773 | 0.20567 | 0.21 | 0.24762 | 0.25 | RANDOM | 54.418 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 1.36 | 0.68 | 1.36 | -4.4 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.22 |
| r_dihedral_angle_3_deg | 19.41 |
| r_dihedral_angle_4_deg | 19.377 |
| r_dihedral_angle_1_deg | 7.185 |
| r_long_range_B_refined | 5.633 |
| r_long_range_B_other | 5.632 |
| r_scangle_other | 2.677 |
| r_mcangle_other | 2.59 |
| r_mcangle_it | 2.589 |
| r_scbond_it | 1.64 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14172 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 540 |
| Heterogen Atoms | 176 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
