2XWK
SiaP R147A mutant in complex with Neu5Ac
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2V4C | PDB ENTRY 2V4C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 277 | 35 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, 15 MM NEU5AC, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0 28.5% PEG 6K,100MM SODIUM MALONATE (PH 7.0)); TEMPERATURE 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.75 | α = 90 |
b = 74.75 | β = 90 |
c = 87.07 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARMOSAIC 225 mm CCD | 2009-10-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 1.49 | 28.36 | 100 | 0.11 | 13.8 | 7.3 | 51332 | 4 | 11.6 |
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 | 1.49 | 1.57 | 100 | 0.61 | 4.2 | 7.3 |
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 2V4C | 1.49 | 28.36 | 48757 | 2575 | 100 | 0.11248 | 0.10973 | 0.16357 | RANDOM | 11.529 |
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] | |
0.05 | -0.46 | 0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.617 |
r_dihedral_angle_3_deg | 12.341 |
r_dihedral_angle_4_deg | 9.299 |
r_scangle_it | 9.04 |
r_scbond_it | 7.017 |
r_dihedral_angle_1_deg | 5.622 |
r_mcangle_it | 4.253 |
r_rigid_bond_restr | 3.489 |
r_mcbond_it | 3.392 |
r_mcbond_other | 1.453 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2432 |
Nucleic Acid Atoms | |
Solvent Atoms | 487 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |