5AOT
Very high resolution structure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5AOS | PDB ENTRY 5AOS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 20 MG/ML OF PROTEIN IN 0.2 M SODIUM ACETATE, 0.1 M CACODYLIC ACID PH 6.5, 30%(W/V) POLYETHYLENE GLYCOL 8000. 30%(V/V) GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 34 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 43.272 | ¦Á = 90 |
b = 45.02 | ¦Â = 90 |
c = 49.453 | ¦Ã = 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 PILATUS 6M | 2014-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.02 | 33.29 | 99.6 | 0.05 | 16.2 | 6.2 | 42277 |
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 | 1.02 | 1.05 | 96.5 | 0.94 | 1.5 | 5.4 |
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 | PDB ENTRY 5AOS | 1.02 | 33.29 | 47545 | 2472 | 99.64 | 0.16472 | 0.16443 | 0.17028 | RANDOM | 14.359 |
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] | |
1.16 | -0.43 | -0.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.36 |
r_sphericity_free | 23.507 |
r_dihedral_angle_3_deg | 11.738 |
r_sphericity_bonded | 11.287 |
r_dihedral_angle_4_deg | 10.626 |
r_dihedral_angle_1_deg | 7.476 |
r_rigid_bond_restr | 2.923 |
r_scbond_it | 2.044 |
r_mcangle_it | 1.66 |
r_angle_refined_deg | 1.613 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 802 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |