3CXH | pdb_00003cxh

Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KB9	PDB entries 1KB9 and 1YEA
experimental model	PDB	1YEA	PDB entries 1KB9 and 1YEA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch (Paraffin oil)	7.5	277	1M Sucrose, 10% DMSO, 20mM Tris pH 7.5, 80mM NaCl, 0.05 % UM, 1 M stigmatellin, 5% PEG 4000, Microbatch (Paraffin oil), temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.45	72.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.54	α = 90
b = 162.97	β = 104.39
c = 194.23	γ = 90

Symmetry
Space Group	P 1 21 1

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 4		2004-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	20	92.7	0.66	12.7	3.2	290829	289871			36.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.7	77.5		0.38	2.8	2.8

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 entries 1KB9 and 1YEA	2.5	19.97	290829	289871	14494	95.9	0.225	0.225	0.225	0.23	0.256	0.26	RANDOM	57.9

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]
18.67		4.94	-9.65		-9.02

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.1
c_scangle_it	2.76
c_mcangle_it	2.28
c_scbond_it	1.86
c_mcbond_it	1.34
c_angle_deg	1.3
c_improper_angle_d	1.22
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	35342
Nucleic Acid Atoms
Solvent Atoms	548
Heterogen Atoms	904

Software

Software
Software Name	Purpose
CNS	refinement
DNA	data collection
XDS	data reduction
XDS	data scaling
AMoRE	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.