5JU9
Structure of a beta-1,4-mannanase, SsGH134, in complex with Man3.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | The protein stock in the buffer of 20 mM sodium phosphate, pH7.2, and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20% PEG6000, 0.15-0.2 M CaCl2, and 0.1 M Na HEPES, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.68 | α = 90 |
b = 53.63 | β = 90 |
c = 82.14 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 6M | 2016-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.97949 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.18 | 44.91 | 97.5 | 16.6 | 7 | 52763 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.18 | 1.21 | 80.2 | 0.558 | 2.4 | 3.7 |
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 | alpha-helical fragment | 1.18 | 44.91 | 50049 | 2647 | 97.39 | 0.1325 | 0.13143 | 0.15313 | RANDOM | 13.909 |
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] | |
0.09 | 0.11 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.944 |
r_sphericity_free | 28.502 |
r_dihedral_angle_4_deg | 23.61 |
r_dihedral_angle_3_deg | 11.877 |
r_sphericity_bonded | 7.764 |
r_dihedral_angle_1_deg | 5.096 |
r_long_range_B_refined | 2.689 |
r_long_range_B_other | 2.688 |
r_scangle_other | 2.158 |
r_scbond_it | 1.702 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1230 |
Nucleic Acid Atoms | |
Solvent Atoms | 162 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
ACORN | phasing |