5AF7

3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Native crystal structure


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Details THE CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES (HAMPTON RESEARCH) BY VAPOUR DIFFUSION IN A HANGING DROP CONFIGURATION FROM 0.1 M BIS-TRIS PH 6.5 AND 10 % PEG 3350 AT A PROTEIN CONCENTRATION OF 10 MG/ML, BY MIXING 2 UL OF THE PROTEIN SOLUTION WITH 2 UL MOTHER LIQUOR.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.67 α = 90
b = 100.65 β = 90
c = 118.57 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-08-17
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) -- PETRA III, EMBL c/o DESY P13 (MX1)

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
1.89 100.65 96.0 0.1 -- -- 3.2 -- 69785 -- 2.0 19.08
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)
1.89 1.93 97.8 0.73 -- 2.0 3.2 --

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 1.89 63.79 -- 1.34 -- 69748 3509 95.31 -- 0.1645 0.1625 0.2017 --
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 1.89 1.9159 -- 140 2668 0.2359 0.2736 -- 97.0
X Ray Diffraction 1.9159 1.9433 -- 149 2695 0.2206 0.2766 -- 98.0
X Ray Diffraction 1.9433 1.9723 -- 135 2661 0.2155 0.2572 -- 97.0
X Ray Diffraction 1.9723 2.0031 -- 130 2687 0.2013 0.2495 -- 97.0
X Ray Diffraction 2.0031 2.0359 -- 133 2671 0.2024 0.2346 -- 97.0
X Ray Diffraction 2.0359 2.0711 -- 135 2655 0.199 0.2522 -- 97.0
X Ray Diffraction 2.0711 2.1087 -- 155 2676 0.1942 0.2735 -- 97.0
X Ray Diffraction 2.1087 2.1493 -- 146 2655 0.1831 0.2362 -- 97.0
X Ray Diffraction 2.1493 2.1932 -- 132 2675 0.1741 0.2207 -- 97.0
X Ray Diffraction 2.1932 2.2408 -- 164 2620 0.1749 0.2112 -- 96.0
X Ray Diffraction 2.2408 2.293 -- 133 2666 0.1695 0.2148 -- 97.0
X Ray Diffraction 2.293 2.3503 -- 129 2661 0.1667 0.2549 -- 96.0
X Ray Diffraction 2.3503 2.4139 -- 164 2628 0.1609 0.1922 -- 96.0
X Ray Diffraction 2.4139 2.4849 -- 125 2675 0.1594 0.1821 -- 96.0
X Ray Diffraction 2.4849 2.5651 -- 126 2658 0.1635 0.2315 -- 96.0
X Ray Diffraction 2.5651 2.6568 -- 145 2649 0.1571 0.2257 -- 96.0
X Ray Diffraction 2.6568 2.7632 -- 141 2628 0.1588 0.1734 -- 95.0
X Ray Diffraction 2.7632 2.8889 -- 151 2650 0.1578 0.2008 -- 95.0
X Ray Diffraction 2.8889 3.0412 -- 159 2617 0.1592 0.1963 -- 95.0
X Ray Diffraction 3.0412 3.2318 -- 142 2625 0.1545 0.178 -- 94.0
X Ray Diffraction 3.2318 3.4813 -- 125 2632 0.1533 0.1896 -- 94.0
X Ray Diffraction 3.4813 3.8316 -- 143 2614 0.1465 0.1661 -- 93.0
X Ray Diffraction 3.8316 4.3859 -- 120 2643 0.1275 0.1812 -- 93.0
X Ray Diffraction 4.3859 5.5253 -- 141 2602 0.1384 0.1643 -- 91.0
X Ray Diffraction 5.5253 63.8263 -- 146 2628 0.1612 0.1823 -- 88.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.3
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.038
f_dihedral_angle_d 13.979
f_bond_d 0.007
f_plane_restr 0.004
f_angle_d 0.994
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5929
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 831

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
Aimless data scaling
PHASER phasing