2IIQ
Crystal structure of Pasteurella multocida sialyltransferase in an open conformation with CMP bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2EX0 | PDB ENTRY 2EX0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 25%, PEG 3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100 streak seeded by apo crystals, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.528 | α = 90 |
b = 61.572 | β = 94.77 |
c = 119.547 | 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 | BRUKER SMART 6000 | 2006-06-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.2 | 59.55 | 99.76 | 0.1001 | 5.35 | 6.16 | 39043 | 38951 | 20.54 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.3 | 100 | 0.2421 | 1.78 | 4884 |
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 2EX0 | 2.3 | 59.55 | 32366 | 1705 | 99.95 | 0.21006 | 0.20766 | 0.25554 | RANDOM | 5.84 |
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] | |
-0.67 | -0.23 | 0.39 | 0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.37 |
r_dihedral_angle_4_deg | 17.027 |
r_dihedral_angle_3_deg | 16.779 |
r_dihedral_angle_1_deg | 6.612 |
r_scangle_it | 1.982 |
r_angle_refined_deg | 1.348 |
r_scbond_it | 1.24 |
r_mcangle_it | 0.814 |
r_mcbond_it | 0.506 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6331 |
Nucleic Acid Atoms | |
Solvent Atoms | 569 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PROTEUM PLUS | data collection |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |
AMoRE | phasing |