5WSC
Crystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, soaked with allosteric activators AMP and Glucose 6-Phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5WRP |
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 ATP, 5 mM AMP, 5 mM D-glucose 6-phosphate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.16 | 61.02 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 124.37 | α = 90 |
b = 124.37 | β = 90 |
c = 144.192 | 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 | CCD | ADSC QUANTUM 210r | 2016-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.95370 | Australian Synchrotron | MX1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 53.85 | 100 | 8.3 | 5.5 | 97539 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.4 | 2.44 | 99.9 | 1.6 | 5.1 |
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 | 5WRP | 2.4 | 53.85 | 92706 | 4790 | 99.96 | 0.18162 | 0.1793 | 0.15 | 0.22696 | 0.2 | RANDOM | 27.566 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
10.11 | 10.11 | -20.23 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.666 |
r_dihedral_angle_4_deg | 20.432 |
r_dihedral_angle_3_deg | 17.274 |
r_dihedral_angle_1_deg | 6.659 |
r_long_range_B_refined | 2.773 |
r_long_range_B_other | 2.771 |
r_mcangle_it | 2.115 |
r_mcangle_other | 2.114 |
r_scangle_other | 2.088 |
r_scbond_it | 1.589 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 14172 |
Nucleic Acid Atoms | |
Solvent Atoms | 335 |
Heterogen Atoms | 195 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |