Engineered CBM X-2 L110F in complex with branched carbohydrate XXXG.
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 4BJ0 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | Large crystals were grown in 9-well glass plates using Hampton sandwich box set-up. |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.3 | 46.59 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 72.977 | α = 90 |
b = 49.856 | β = 90 |
c = 45.091 | γ = 90 |
Symmetry |
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Space Group | P 21 21 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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2 | 1 | neutron | 293 | IMAGE PLATE | FUJI | | 2014-11-25 | M | SINGLE WAVELENGTH |
1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | | 2014-10-28 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 2.66 | FRM II | BIODIFF |
1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | 1.04 | MAX II | I911-2 |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 |
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2 | 1.6 | 45 | 91.1 | 0.041 | | | | | | 6.6 | 3 | | 20530 | | | |
1 | 1.6 | 29.3 | 97.7 | 0.093 | | | | | | 28.6 | 5.5 | | 21610 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.6 | 1.7 | | 0.231 | | | | | | 7.8 | 5.5 | 3389 |
2 | 1.6 | 1.65 | | 0.449 | | | | | | 1.8 | 2.5 | 1485 |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.6 | 45 | | | | 20512 | 1027 | 91.09 | | 0.2239 | 0.2225 | 0.25 | | |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.606 | 29.445 | | | | 21609 | 1081 | 97.69 | | 0.1648 | 0.1628 | 0.204 | | |
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] |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 22.277 |
f_dihedral_angle_d | 22.277 |
f_angle_d | 1.268 |
f_angle_d | 1.268 |
f_chiral_restr | 0.08 |
f_chiral_restr | 0.08 |
f_bond_d | 0.01 |
f_bond_d | 0.01 |
f_plane_restr | 0.006 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1260 |
Nucleic Acid Atoms | |
Solvent Atoms | 60 |
Heterogen Atoms | 73 |
Protein Atoms | 1260 |
Nucleic Acid Atoms | |
Solvent Atoms | 60 |
Heterogen Atoms | 73 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Coot | model building |