8HCJ
Structure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from pseudopedobacter saltans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NOV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293.15 | 18% PEG 3350, 5% PROPANOL, 0.15M IMIDAZOLE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.34 | α = 102.734 |
b = 89.662 | β = 93.985 |
c = 138.437 | γ = 98.237 |
Symmetry | |
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Space Group | P 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 | 273 | PIXEL | DECTRIS PILATUS3 2M | 2022-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.96546 | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.5 | 134.29 | 95 | 0.08 | 0.1 | 0.07 | 0.94 | 0.04 | 1.92 | 103346 | 30.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.5 | 2.56 | 97 | 0.02 | 0.28 | 0.19 | 0.93 | 2.01 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4NOV | 2.566 | 134.29 | 103343 | 5180 | 95.375 | 0.166 | 0.1634 | 0.2091 | 33.093 |
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] | |
2.558 | 1.763 | 0.582 | -0.804 | 0.843 | -2.466 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 19.327 |
r_dihedral_angle_6_deg | 17.669 |
r_lrange_it | 10.506 |
r_scangle_it | 7.745 |
r_dihedral_angle_1_deg | 6.808 |
r_mcangle_it | 6.384 |
r_scbond_it | 5.791 |
r_dihedral_angle_2_deg | 4.871 |
r_mcbond_it | 4.519 |
r_angle_refined_deg | 1.494 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 27430 |
Nucleic Acid Atoms | |
Solvent Atoms | 1325 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |