8IAV
Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with fructose 1,6-bisphosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 9%PEG3350,150mM NH4Cl, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM FBP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 217.032 | α = 90 |
b = 86.789 | β = 103.22 |
c = 129.857 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror. | 2022-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.900 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.59 | 47.69 | 99.2 | 0.05 | 0.055999999999999994 | 0.9990000000000001 | 18.21 | 5.19 | 72422 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.59 | 2.75 | 0.9540000000000001 | 1.06 | 0.89 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.59 | 47.69 | 68784 | 3621 | 99.22 | 0.23704 | 0.23388 | 0.29776 | RANDOM | 99.559 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
4.01 | 5.57 | -7.93 | 1.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.443 |
r_dihedral_angle_4_deg | 21.027 |
r_dihedral_angle_3_deg | 19.731 |
r_long_range_B_refined | 14.32 |
r_long_range_B_other | 14.32 |
r_scangle_other | 9.656 |
r_mcangle_it | 9.319 |
r_mcangle_other | 9.319 |
r_dihedral_angle_1_deg | 7.04 |
r_scbond_other | 6.416 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13864 |
Nucleic Acid Atoms | |
Solvent Atoms | 18 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
MOLREP | phasing |