7ESN
Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, H105F Rha-GlcA complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277.15 | 1.6 M ammonium sulfate, 0.1 M Na-acetate (pH 4.6), Crystal was soaked into 20 mM Rha-GlcA and 20 % (v/v) glycerol at 298 K for 1 min |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.82 | 74.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.242 | α = 90 |
b = 190.137 | β = 90 |
c = 80.11 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 PILATUS3 S 6M | 2019-06-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.000 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.42 | 105.75 | 100 | 0.997 | 17.7 | 6.8 | 37476 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.42 | 2.51 | 0.875 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.42 | 46.3 | 35629 | 1845 | 99.95 | 0.209 | 0.2074 | 0.2417 | RANDOM | 51.577 |
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] | |
0.32 | -0.12 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.777 |
r_dihedral_angle_4_deg | 20.639 |
r_dihedral_angle_3_deg | 16.533 |
r_dihedral_angle_1_deg | 8.405 |
r_angle_refined_deg | 1.347 |
r_angle_other_deg | 1.132 |
r_chiral_restr | 0.048 |
r_gen_planes_refined | 0.004 |
r_bond_refined_d | 0.003 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3471 |
Nucleic Acid Atoms | |
Solvent Atoms | 144 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |