2XCU
Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, complex with CMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND RESERVOIR (100 MM TRIS-HCL, PH 8.5, 35-40% (V/V) PEG 400, 200 MM NA-CITRATE, 50 MM 2-MERCAPTOETHANOL); SOAKING CRYSTALS IN 100 MM TRIS-HCL (PH 8.5), 36% (V/V) PEG 400, 200 MM NA-CITRATE AND 10 MM CMP FOR FOUR DAYS |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 131.77 | α = 90 |
b = 44.67 | β = 97.15 |
c = 143.64 | 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 | MARRESEARCH SX-165 | 2009-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-2 | MAX II | I911-2 |
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 | 2.42 | 31.85 | 97.2 | 0.04 | 21.3 | 3.6 | 62789 | 2 | 47.57 |
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 | 2.42 | 2.55 | 88.3 | 0.14 | 6.8 | 3 |
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 2XCI | 2.42 | 31.22 | 59636 | 3139 | 97.22 | 0.20478 | 0.20236 | 0.25087 | RANDOM | 29.993 |
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] | |
-2.6 | -0.3 | 6.95 | -4.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.343 |
r_dihedral_angle_4_deg | 19.815 |
r_dihedral_angle_3_deg | 17.634 |
r_dihedral_angle_1_deg | 6.555 |
r_scangle_it | 3.501 |
r_scbond_it | 2.027 |
r_angle_refined_deg | 1.587 |
r_mcangle_it | 1.407 |
r_mcbond_it | 0.722 |
r_chiral_restr | 0.104 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11488 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 230 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |