5E5N
Ketosynthase from module 6 of the bacillaene synthase from Bacillus subtilis 168 (C167S mutant, crystal form 1)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NA1 | PksKS2 (4NA1) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 15 mg/ml protein in 150 mM NaCl and 20 mM HEPES pH 7.5 mixed 1:1 in 1.7 M LiSO4 and 100 mM Tris pH 8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.436 | α = 90 |
b = 108.194 | β = 96.43 |
c = 151.846 | 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 | PIXEL | PSI PILATUS 6M | 2013-11-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 150 | 99.2 | 2.5 | 2.1 | 183336 |
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 | PksKS2 (4NA1) | 2 | 150 | 183336 | 9722 | 99.2 | 0.2039 | 0.2022 | 0.23649 | RANDOM | 44.025 |
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] | |
0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.474 |
r_dihedral_angle_4_deg | 17.904 |
r_dihedral_angle_3_deg | 14.886 |
r_long_range_B_refined | 10.977 |
r_long_range_B_other | 10.964 |
r_scangle_other | 8.788 |
r_dihedral_angle_1_deg | 6.771 |
r_mcangle_it | 6.546 |
r_mcangle_other | 6.546 |
r_scbond_it | 6.409 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17239 |
Nucleic Acid Atoms | |
Solvent Atoms | 1358 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |