3SFE | pdb_00003sfe

crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and thiabendazole

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZOY	PDB ENTRY 1ZOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	290	0.5% n-nonyl-D-maltoside, 1.7mM n-decyl-D-maltoside, 25mM HEPES, 5% PEG 4000, 3% 1,6-hexanediol, 100mM NaCl, 10mM CaCl2, 200mM sucrose, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.51	65.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.71	α = 90
b = 83.42	β = 90
c = 294.01	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	CCD	ADSC QUANTUM 315		2008-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.000	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8	50	94.6	0.1	12	4.5	43960	41586		-1	63.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	81.2		0.427	1.7	3.5	2859

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZOY	2.81	50	41586	32353	1717	78.06	0.274	0.21684	0.21405	0.22	0.26985	0.27	RANDOM	56.462

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]
1.07			-1.68		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.834
r_dihedral_angle_3_deg	18.752
r_dihedral_angle_4_deg	14.696
r_dihedral_angle_1_deg	5.374
r_angle_refined_deg	1.243
r_scangle_it	1.019
r_mcangle_it	0.608
r_scbond_it	0.58
r_mcbond_it	0.327
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.834
r_dihedral_angle_3_deg	18.752
r_dihedral_angle_4_deg	14.696
r_dihedral_angle_1_deg	5.374
r_angle_refined_deg	1.243
r_scangle_it	1.019
r_mcangle_it	0.608
r_scbond_it	0.58
r_mcbond_it	0.327
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8489
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	138

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.