6ES9 | pdb_00006es9

Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N5F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	1 part protein solution (20.0 mg/mL in 20 mM Tris-HCl, pH 7.9, 200 mM sodium chloride, 1.5 mM FAD, 3 mM mesaconyl-CoA) + 1 part buffer (0.1 M Tris-HCl, pH 8.0, 30% w/v PEG5000 MME, 200 mM lithium sulfate)

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.596	α = 90
b = 105.193	β = 90
c = 138.939	γ = 90

Symmetry
Space Group	P 21 21 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		2017-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.979026	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	1.37	17.573	100	0.065	0.07	0.026	0.999	15.2	7.4		249985			15.84

Highest Resolution Shell
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	1.37	1.44	100		1.103	1.103	1.187	0.436	0.632	1.6	7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4N5F	1.37	17.573	1.33	249828	2000	99.98	0.176	0.176	0.18	0.1847	0.19	22.0831

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	20.516
f_angle_d	1.405
f_chiral_restr	0.098
f_bond_d	0.016
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8328
Nucleic Acid Atoms
Solvent Atoms	1389
Heterogen Atoms	180

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
TRUNCATE	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

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.