3DTU | pdb_00003dtu

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GSM	PDB entry 2GSM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	277	24% PEG-400, 5mM deoxycholic acid , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.243	α = 90
b = 132.052	β = 90
c = 167.966	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	MARMOSAIC 300 mm CCD		2007-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9785	APS	21-ID-G

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	2.15	50	96.8	0.069	21.9	6.6	150058	145257

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)
	2.15	2.33	77.6		0.513	2.1	3.8	11510

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		THROUGHOUT	PDB entry 2GSM	2.15	40	148964	144361	3612	96.91	0.184	0.184	0.184	0.1844	0.212	0.2146	RANDOM	38.516

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]
-1.73			-0.82		2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.681
r_dihedral_angle_4_deg	16.208
r_dihedral_angle_3_deg	13.853
r_dihedral_angle_1_deg	5.681
r_scangle_it	1.965
r_scbond_it	1.376
r_angle_refined_deg	1.215
r_mcangle_it	0.983
r_mcbond_it	0.594
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.681
r_dihedral_angle_4_deg	16.208
r_dihedral_angle_3_deg	13.853
r_dihedral_angle_1_deg	5.681
r_scangle_it	1.965
r_scbond_it	1.376
r_angle_refined_deg	1.215
r_mcangle_it	0.983
r_mcbond_it	0.594
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.127
r_metal_ion_refined	0.108
r_chiral_restr	0.088
r_symmetry_hbond_refined	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12565
Nucleic Acid Atoms
Solvent Atoms	636
Heterogen Atoms	780

Software

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