6II0
Crystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio vulnificus MO6-24/O
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6II6 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 12% PEG 3000, 0.1M Na2HPO4/citric acid (pH 4.2), 0.4M NaCl, 10% glycerol |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.46 | 50 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 78.64 | α = 90 |
b = 78.64 | β = 90 |
c = 450.008 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 270 | 2018-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.9793 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.36 | 50 | 97.3 | 6.1 | 5 | 60806 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.36 | 2.4 | 0.643 | 0.273 | 0.77 |
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 | 6II6 | 2.36 | 50 | 59323 | 3193 | 97.28 | 0.18517 | 0.18242 | 0.23662 | RANDOM | 39.146 |
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] | |
0.11 | 0.06 | 0.11 | -0.37 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.163 |
r_dihedral_angle_4_deg | 18.791 |
r_dihedral_angle_3_deg | 15.994 |
r_long_range_B_refined | 9.411 |
r_long_range_B_other | 9.41 |
r_dihedral_angle_1_deg | 7.167 |
r_scangle_other | 6.557 |
r_mcangle_it | 5.681 |
r_mcangle_other | 5.68 |
r_scbond_it | 4.356 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9567 |
Nucleic Acid Atoms | |
Solvent Atoms | 363 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |
Coot | model building |
REFMAC | refinement |