7K74
Crystal Structure of Fructose-1,6-bisphosphatase, type I, from Stenotrophomonas maltophilia K279a
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NUY | pdb entry 1nuy as per Morda |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 287 | Rigaku Reagents JCSG+ screen, condition h12: 45% (V/V) MPD, 200mM Ammonium acetate, 100mM HEPES free acid / NaOH pH 7.5: StmaA.17936.a.B1.PW38784 at 22.75mg/ml + 4mM fructose-1,6-bisphosphate: tray: 315242h12, cryo: direct: puck: uog3-7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.04 | α = 90 |
b = 125.73 | β = 90 |
c = 158.45 | 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 | RAYONIX MX-300 | Beryllium Lenses | 2018-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 50 | 99.7 | 0.078 | 0.084 | 0.999 | 12.72 | 7.359 | 77671 | 40.704 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.2 | 2.26 | 99.7 | 0.551 | 0.592 | 0.971 | 3.45 | 7.474 |
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 | pdb entry 1nuy as per Morda | 2.2 | 37.78 | 1.34 | 76881 | 1973 | 98.82 | 0.2145 | 0.2135 | 0.251 | 0 | 41.87 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.9353 |
f_angle_d | 0.8813 |
f_chiral_restr | 0.051 |
f_plane_restr | 0.0083 |
f_bond_d | 0.0073 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9714 |
Nucleic Acid Atoms | |
Solvent Atoms | 465 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MoRDa | phasing |
PHENIX | model building |
Coot | model building |