6OEW
Structure of a Cytidylyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Molecular Dimensions Morpheus screen, a6: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM of each magnesium chloride and calcium chloride, 100mM MOPS/HEPES-Na pH 7.5: LpboA.19557.c.B1.PS38542 at 24.74mg/ml: cryo: direct: tray 306886 a6: puck ogn0-8. For experimental phasing, a crystal from Morpheus screen a3 (10% w/v PEG 4000, 20% v/v glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM MES/imidazole pH 6.5: LpboA.19557.c.B1.PS38542 at 24.74mg/ml) was incubated for 20sec in a solution of 92.5% reservoir and 7.5% 5M Sodium iodide in ethylene glycol, and vitrified: tray: 306886 a3: puck: kzx0-4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.51 | α = 90 |
b = 65.51 | β = 90 |
c = 261.93 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | RAYONIX MX-300 | 2019-02-28 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2019-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 1.85 | 43.671 | 100 | 0.054 | 0.057 | 0.999 | 22.16 | 9.57 | 50144 | 38.04 |
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 | 1.85 | 1.9 | 100 | 0.581 | 0.614 | 0.954 | 3.27 | 9.747 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1.85 | 43.671 | 1.35 | 49962 | 1946 | 99.86 | 0.1731 | 0.1714 | 0.2147 | 0 | 41.3441 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.228 |
f_angle_d | 0.989 |
f_chiral_restr | 0.06 |
f_bond_d | 0.009 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3860 |
Nucleic Acid Atoms | |
Solvent Atoms | 366 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
PARROT | phasing |
ARP/wARP | model building |
BUCCANEER | model building |
Coot | model building |