4D3L
SeMet structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1 in the orthorhombic form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 0.2 M SODIUM CITRATE, 2 M AMMONIUM SULPHATE. CRYOPROTECTANT USED PARATONE N, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.19 | 61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.302 | α = 90 |
b = 103.345 | β = 90 |
c = 109.067 | γ = 90 |
Symmetry | |
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Space Group | I 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2013-07-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 2 | 43.63 | 100 | 0.16 | 5.2 | 5.7 | 37050 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2 | 2.11 | 69.9 | 0.69 | 0.9 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | SAD | THROUGHOUT | NONE | 2 | 75.02 | 35182 | 1848 | 93.62 | 0.21362 | 0.21201 | 0.24523 | RANDOM | 35.825 |
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] | |
-0.1 | 0.81 | -0.71 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.992 |
r_dihedral_angle_4_deg | 26.194 |
r_dihedral_angle_3_deg | 13.868 |
r_dihedral_angle_1_deg | 6.454 |
r_mcangle_it | 2.751 |
r_scbond_it | 2.643 |
r_mcbond_other | 1.857 |
r_mcbond_it | 1.856 |
r_angle_refined_deg | 1.414 |
r_angle_other_deg | 1.037 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3054 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
PARROT | model building |
Aimless | data scaling |
SHELX | phasing |
CCP4 | phasing |
PHASER | phasing |
PARROT | phasing |
REFMAC | refinement |