5MDS
Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in complex with chitotetraose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5MDO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 28% (w/v) PEG 400, 0.2 M sodium acetate, 0.1 M MES pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.31 | 71.46 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 250.01 | ¦Á = 90 |
b = 145.047 | ¦Â = 94.8 |
c = 55.158 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 PILATUS 6M | 2015-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.979490 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.6 | 125.35 | 93.4 | 0.09 | 0.081 | 8.4 | 2.9 | 56059 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.6 | 2.68 | 95.1 | 0.777 | 0.699 | 1.1 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | 5MDO | 2.6 | 125.35 | 54404 | 1652 | 93.15 | 0.22201 | 0.22126 | 0.24749 | RANDOM | 62.644 |
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] | |
2.3 | -1.36 | -0.79 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.634 |
r_dihedral_angle_4_deg | 17.162 |
r_dihedral_angle_3_deg | 15.183 |
r_dihedral_angle_1_deg | 7.721 |
r_long_range_B_other | 3.825 |
r_long_range_B_refined | 3.823 |
r_scangle_other | 2.699 |
r_angle_refined_deg | 2.085 |
r_scbond_other | 1.752 |
r_scbond_it | 1.751 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7995 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 171 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |