8GFC
Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Fv17b inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6CF9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.9 | 293 | 0.1 M sodium citrate pH 5.9 and 26% (v/v) PEG 600. Protein buffer was 10 mM HEPES pH 8.0, 200 mM ammonium acetate. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.6 | 65.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 176.494 | α = 90 |
b = 176.494 | β = 90 |
c = 176.494 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2022-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-1 | 0.9795 | SSRL | BL12-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.48 | 39.47 | 99.3 | 0.148 | 0.156 | 0.048 | 0.995 | 8.2 | 10.2 | 32058 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.48 | 2.59 | 94.1 | 0.992 | 1.049 | 0.336 | 0.736 | 9.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 6CF9 | 2.48 | 39.47 | 30390 | 1659 | 99.3 | 0.1802 | 0.1782 | 0.2149 | RANDOM | 66.861 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
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 | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 17.165 |
r_dihedral_angle_2_deg | 12.857 |
r_dihedral_angle_1_deg | 6.752 |
r_angle_refined_deg | 1.479 |
r_angle_other_deg | 0.486 |
r_chiral_restr | 0.067 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.002 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4251 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 43 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |