6ER4
Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VW2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2M ammonium chloride with 20% PEG 8000 crystal growth time was improved using micro-seeding Crystals were cryoprotected using the crystallisation condition supplemented with 25% (w/w) glycerol crystal was co-crystallised with 10mM 2,6 sialyllactose and soaked with 100mM 2,6 sialyllactose immediately prior to freezing |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.74 | α = 90 |
b = 72.2 | β = 103.88 |
c = 51.41 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | RIGAKU SATURN 944+ | 2014-07-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | ||||||
1 | 1.3 | 49.91 | 83.9 | 0.031 | 0.034 | 0.013 | 32 | 5.1 | 70604 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.303 | 1.34 | 13.6 | 0.148 | 0.148 | 0.143 | 5.5 | 1.4 |
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 | 2vw2 | 1.3 | 49.91 | 67097 | 3481 | 83.8 | 0.1097 | 0.1084 | 0.1345 | RANDOM | 11.479 |
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] | |
0.48 | -0.37 | -0.16 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.246 |
r_sphericity_free | 31.802 |
r_dihedral_angle_4_deg | 19.417 |
r_dihedral_angle_3_deg | 11.265 |
r_sphericity_bonded | 7.215 |
r_dihedral_angle_1_deg | 7.193 |
r_rigid_bond_restr | 2.375 |
r_angle_refined_deg | 1.712 |
r_angle_other_deg | 1.65 |
r_mcangle_it | 1.034 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2896 |
Nucleic Acid Atoms | |
Solvent Atoms | 488 |
Heterogen Atoms | 123 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |