5VE2
Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalteromonas atlantica T6c at 2.3 A resolution.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | 0.2 ul of 20 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the JCSG+ condition #89 (0.2M ammonium acetate, 0.1M Bis-Tris pH 5.5, 45% (v/v) MPD) and equilibrated against 0.9 M NaCl solution in 96 Well 3 drop Crystallization Plate (SwissCi). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.66 | α = 90 |
b = 160.141 | β = 90.12 |
c = 136.271 | 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 | Beryllium Lenses | 2013-11-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.987 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.3 | 38 | 95.2 | 0.084 | 0.084 | 0.103 | 0.059 | 6 | 3 | 142189 | -3 | 37.7 |
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 | 2.3 | 2.34 | 97.5 | 0.336 | 0.336 | 0.409 | 0.23 | 0.933 | 3.3 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.3 | 38 | 134973 | 7178 | 95.14 | 0.2079 | 0.2051 | 0.2576 | RANDOM | 47.067 |
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] | |
-2.59 | -0.05 | 1.25 | 1.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.677 |
r_dihedral_angle_4_deg | 18.907 |
r_dihedral_angle_3_deg | 12.211 |
r_dihedral_angle_1_deg | 5.345 |
r_angle_refined_deg | 1.436 |
r_angle_other_deg | 0.96 |
r_chiral_restr | 0.083 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 22496 |
Nucleic Acid Atoms | |
Solvent Atoms | 1998 |
Heterogen Atoms | 67 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
HKL-3000 | data scaling |
SHELXD | phasing |
DM | phasing |
MLPHARE | phasing |
HKL-3000 | phasing |
BUCCANEER | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
DENZO | data reduction |
SCALEPACK | data scaling |