8ZLY
Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and UDP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL44XU |
Synchrotron site | SPring-8 |
Beamline | BL44XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-12-04 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.900 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 115.809, 403.204, 113.593 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.160 - 1.890 |
R-factor | 0.16721 |
Rwork | 0.165 |
R-free | 0.20472 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.011 |
RMSD bond angle | 1.719 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.170 | 48.170 | 2.000 |
High resolution limit [Å] | 1.890 | 5.630 | 1.890 |
Rmerge | 0.062 | 0.033 | 0.307 |
Rmeas | 0.079 | 0.040 | 0.399 |
Number of reflections | 423736 | 9892 | 51387 |
<I/σ(I)> | 6.23 | ||
Completeness [%] | 99.8 | ||
Redundancy | 13.34 | ||
CC(1/2) | 0.996 | 0.998 | 0.856 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 298 | 60 mM HEPES pH7.3, 75 mM NaCl, 75 mM KCl, 10 mM MgCl2, 75 mM Na formate, 14 % PEG3350, 10 mM oxalate, 10 mM FBP, 5 mM UDP |