8CIW | pdb_00008ciw

Methylsuccinyl-CoA dehydrogenase from Pseudomonas migulae with bound FAD and (2S)-methylsuccinyl-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ES9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	Enzyme (20 mg/mL) in 25 mM MOPS pH 7.5 and 0.2 M NaCl was mixed in a 1:1 ratio with crystallization condition (0.2 M ammonium citrate pH 5.0, 20% (w/v) PEG 3350). Soaking and cryoprotection of crystals was performed by adding methylsuccinyl-CoA and PEG200 to final concentrations of 16 mM and 40% (v/v), respectively, before crystals were plunge frozen in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.805	α = 90
b = 169.563	β = 90
c = 118.39	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim 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	1.93	25.01	99.7	0.124	0.034	0.999	14.6	13.2		105292

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.93	2.03		98.6	1.213	0.337	0.892		12.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.93	25.01	0.97	105172	1997	99.7	0.1744	0.1739	0.17	0.2027	0.2

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.643
f_angle_d	0.967
f_chiral_restr	0.052
f_bond_d	0.009
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8632
Nucleic Acid Atoms
Solvent Atoms	567
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.