8UZ8
Crystal Structure of CiaD from Campylobacter jejuni (C-terminal fragment, Orthorhombic P form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Morpheus Fusion A2: 20% v/v Ethylene glycol; 10 % w/v PEG 8000, 0.04M Imidazole; 0.06M MES monohydrate (acid), pH 6.5, 0.02M 1,6-Hexanediol; 0.02M 1-Butanol, 0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol, 5 mM MnCl2, 5 mM CoCl2 , 5 mM NiCl2, 5 mM Zn(OAc)2 . CajeA.19923.a.LA1.PB00122 at 27 mg/mL. Plate: 13443 well A2, drop 1. Puck: PSL-1703, Cryo: Direct. Mass spectrometry indicated a truncated fragment of the full-length protein ~7,142 Da-7,161 Da. The electron density best fit residues approximately spanning Ser 106-Lys 165. |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.959 | α = 90 |
b = 139.933 | β = 90 |
c = 21.196 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | PIXEL | DECTRIS EIGER2 XE 9M | 2023-10-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9795 | NSLS-II | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.45 | 46.96 | 99.9 | 0.09 | 0.098 | 0.04 | 0.998 | 11.8 | 6.1 | 5660 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.45 | 2.51 | 100 | 0.779 | 0.851 | 0.337 | 0.892 | 6.3 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.45 | 44.52 | 1.35 | 5613 | 274 | 99.7 | 0.2152 | 0.2133 | 0.2473 |
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 | 12.209 |
f_angle_d | 0.752 |
f_chiral_restr | 0.039 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 962 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
Arcimboldo | phasing |