4EU6

Succinyl-CoA:acetate CoA-transferase (AarCH6) in complex with CoA, acetate, and covalent acetylglutamyl anhydride and glutamyl-CoA thioester adducts



X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 298.0
Details 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM acetyl-CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.17 α = 90
b = 110.41 β = 90
c = 119.82 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-07-23
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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
1.99 50 99.7 0.11 0.11 -- 12.7 61848 61848 -- -3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.99 2.02 99.1 0.53 0.53 7.2 12.1 3022

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.988 34.745 -- 0.0 -- 61777 3092 99.6 -- 0.1666 0.1644 0.2085 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.9878 2.0189 2690 141 2549 0.1654 0.2431 -- 97.0
X Ray Diffraction 2.0189 2.052 2754 128 2626 0.1719 0.2351 -- 99.0
X Ray Diffraction 2.052 2.0873 2755 138 2617 0.1755 0.2218 -- 99.0
X Ray Diffraction 2.0873 2.1253 2776 145 2631 0.1688 0.2477 -- 99.0
X Ray Diffraction 2.1253 2.1662 2778 130 2648 0.1716 0.2346 -- 99.0
X Ray Diffraction 2.1662 2.2104 2738 150 2588 0.169 0.2312 -- 99.0
X Ray Diffraction 2.2104 2.2584 2810 141 2669 0.1717 0.222 -- 99.0
X Ray Diffraction 2.2584 2.3109 2756 144 2612 0.1713 0.2364 -- 100.0
X Ray Diffraction 2.3109 2.3687 2783 138 2645 0.1701 0.2638 -- 100.0
X Ray Diffraction 2.3687 2.4328 2776 131 2645 0.1677 0.2104 -- 99.0
X Ray Diffraction 2.4328 2.5043 2794 138 2656 0.1638 0.1911 -- 100.0
X Ray Diffraction 2.5043 2.5851 2808 152 2656 0.1701 0.2366 -- 100.0
X Ray Diffraction 2.5851 2.6775 2792 128 2664 0.1862 0.2288 -- 100.0
X Ray Diffraction 2.6775 2.7847 2804 144 2660 0.1837 0.2437 -- 100.0
X Ray Diffraction 2.7847 2.9113 2827 141 2686 0.1782 0.2166 -- 100.0
X Ray Diffraction 2.9113 3.0647 2829 133 2696 0.1792 0.2192 -- 100.0
X Ray Diffraction 3.0647 3.2566 2819 154 2665 0.1671 0.2038 -- 100.0
X Ray Diffraction 3.2566 3.5078 2825 129 2696 0.1605 0.1943 -- 100.0
X Ray Diffraction 3.5078 3.8604 2839 149 2690 0.1491 0.209 -- 100.0
X Ray Diffraction 3.8604 4.4181 2892 141 2751 0.1443 0.1563 -- 100.0
X Ray Diffraction 4.4181 5.5626 2894 147 2747 0.1459 0.1819 -- 100.0
X Ray Diffraction 5.5626 34.7502 3038 150 2888 0.1675 0.1888 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.8315
Anisotropic B[1][1] -1.1168
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.5971
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.4803
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.423
f_plane_restr 0.005
f_chiral_restr 0.069
f_angle_d 1.047
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7767
Nucleic Acid Atoms 0
Heterogen Atoms 107
Solvent Atoms 595

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction