8XW8
Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and GDP
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 | 2023-10-12 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.900 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 123.335, 256.080, 88.575 |
Unit cell angles | 90.00, 90.04, 90.00 |
Refinement procedure
Resolution | 47.300 - 2.000 |
R-factor | 0.19985 |
Rwork | 0.198 |
R-free | 0.23364 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.019 |
RMSD bond angle | 1.832 |
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] | 47.300 | 47.300 | 2.120 |
High resolution limit [Å] | 2.000 | 5.950 | 2.000 |
Rmerge | 0.112 | 0.037 | 0.912 |
Rmeas | 0.120 | 0.040 | 0.985 |
Number of reflections | 181214 | 6961 | 28831 |
<I/σ(I)> | 16.79 | ||
Completeness [%] | 97.9 | ||
Redundancy | 7.2 | ||
CC(1/2) | 0.998 | 0.999 | 0.821 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 10mM HEPES pH7.5, 250mM NaCl, 75mM KCl, 20% PEG1000, 5% glycerol, 50mM tricine pH8.0, 10mM Oxalate, 10mM FBP, 5mM GDP |