7JS3
Structure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6AYU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.8 | 298 | 20 mM Tricine pH 7.8, 50 mM KCl, 1 mM MgCl2, 0.1 mM DTT, 15% glycerol; Composition of reservoir solution 0.2 M sodium formate, 20% PEG 3350; Volume and ratio of drop 22.4 uL (1:1) Volume of reservoir (ul) 100 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 51.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.296 | α = 90 |
b = 100.169 | β = 90.003 |
c = 92.021 | 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 | MARMOSAIC 300 mm CCD | 2017-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.92456 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | CC (Half) | 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 | 2.4 | 40 | 98.9 | 0.106 | 0.106 | 0.991 | 24.6 | 3.6 | 53682 | 1 | 1 | 42.9 |
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) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.4 | 2.44 | 97.5 | 0.531 | 0.531 | 0.531 | 0.276 | 0.673 | 3.2 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 6ayu | 2.4 | 38.11 | 1 | 53662 | 2732 | 98.747 | 0.155 | 0.1534 | 0.193 | 2732 | 48.033 |
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] | |
-5.067 | -3.658 | -0.204 | 5.271 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.764 |
r_dihedral_angle_3_deg | 19.094 |
r_dihedral_angle_4_deg | 17.373 |
r_dihedral_angle_1_deg | 13.49 |
r_lrange_it | 7.692 |
r_lrange_other | 7.692 |
r_scangle_it | 5.503 |
r_scangle_other | 5.503 |
r_mcangle_it | 5.429 |
r_mcangle_other | 5.429 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9624 |
Nucleic Acid Atoms | |
Solvent Atoms | 172 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |