5HL8
1.93 Angstrom resolution crystal structure of a pullulanase-specific type II secretion system integral cytoplasmic membrane protein GspL (C-terminal fragment; residues 309-397) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | protein: 9.7 mg/mL 10 mM Tris-HCl pH 8.3 crystallization: The Classics II Suite conditions E7 (#55): 0.05 M MgCl2, 0.1 M HEPES pH 7.5, 30 % (v/v) PEG 550 MME cryo: crystallization conditions |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 34.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.375 | α = 90 |
b = 51.284 | β = 90 |
c = 117.021 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | CCD | MARMOSAIC 300 mm CCD | C(111) | 2015-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.93 | 30 | 99.9 | 0.069 | 58.1 | 14.4 | 23407 | -3 | 28.7 |
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 | 1.93 | 1.96 | 100 | 0.588 | 5.7 | 14.7 |
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 | SAD | THROUGHOUT | 1.93 | 26.44 | 22151 | 1203 | 99.77 | 0.22899 | 0.22621 | 0.28137 | RANDOM | 45.834 |
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] | |
3.18 | -0.52 | -2.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.516 |
r_dihedral_angle_4_deg | 13.686 |
r_dihedral_angle_3_deg | 9.642 |
r_dihedral_angle_1_deg | 3.445 |
r_angle_refined_deg | 1.65 |
r_angle_other_deg | 1.302 |
r_chiral_restr | 0.094 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2412 |
Nucleic Acid Atoms | |
Solvent Atoms | 89 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
Coot | model building |