4IIU
Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Escherichia coli strain CFT073 complexed with NADP+ at 2.1 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3OSU | PDB ENTRY 3OSU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 289 | 0.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.541 | α = 90 |
b = 128.541 | β = 90 |
c = 125.938 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | ADSC QUANTUM 210r | MIRRORS | 2012-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9792 | APS | 19-BM |
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 | 2.1 | 50 | 100 | 0.062 | 45.3 | 11.2 | 68701 | -3 | 26.1 |
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 | 2.1 | 2.14 | 100 | 0.819 | 3.5 | 10.6 | 3403 |
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 3OSU | 2.1 | 39.94 | 67856 | 3427 | 98.66 | 0.1692 | 0.1679 | 0.1925 | RANDOM | 34.3943 |
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] | |
-0.43 | -0.43 | -0.43 | 1.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.52 |
r_dihedral_angle_4_deg | 14.55 |
r_dihedral_angle_3_deg | 13.193 |
r_dihedral_angle_1_deg | 5.396 |
r_angle_refined_deg | 1.448 |
r_angle_other_deg | 1.03 |
r_chiral_restr | 0.072 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7016 |
Nucleic Acid Atoms | |
Solvent Atoms | 495 |
Heterogen Atoms | 192 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
BALBES | phasing |