3AE8 | pdb_00003ae8

Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Isopropoxy-phenyl)-2-trifluoromethylbenzamide

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	293	25mM HEPES-NAOH, 8% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.655	α = 90
b = 83.994	β = 90
c = 295.317	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	MAC Science DIP-2040		2008-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90000	SPring-8	BL44XU

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	3.4	50	83.9	0.086	11.268	3.8		21305

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	3.4	3.52	87.5		0.44	2.28	3.8	2165

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZOY	3.4	48.31	21173	1067	83.6	0.242	0.239	0.24	0.288	0.29	RANDOM	99.758

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]
0.46			-0.03		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.474
r_dihedral_angle_3_deg	15.376
r_dihedral_angle_4_deg	9.797
r_dihedral_angle_1_deg	3.909
r_angle_refined_deg	0.853
r_scangle_it	0.177
r_mcangle_it	0.16
r_scbond_it	0.095
r_mcbond_it	0.089
r_chiral_restr	0.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.474
r_dihedral_angle_3_deg	15.376
r_dihedral_angle_4_deg	9.797
r_dihedral_angle_1_deg	3.909
r_angle_refined_deg	0.853
r_scangle_it	0.177
r_mcangle_it	0.16
r_scbond_it	0.095
r_mcbond_it	0.089
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8480
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	182

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
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.