1AR1 | pdb_00001ar1

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		FOUR PROTEIN SUBUNITS CONTAINING CYTOCHROME C OXIDASE FROM PARACOCCUS DENITRIFICANS (NATURE 376: 660-669)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
4.8	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.5	α = 90
b = 151	β = 90
c = 156.7	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	277	CCD	PRINCETON 2K	COLLIMATING AND FOCUSSING MIRROR	1997-01-31	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.7	50	93.8	0.068	13.4	3.4		57373			44.2

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)
	2.7	2.8	79.7		0.332	4	2.5

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	FOUR PROTEIN SUBUNITS CONTAINING CYTOCHROME C OXIDASE FROM PARACOCCUS DENITRIFICANS (NATURE 376: 660-669)	2.7	30	2	57373	2910	93.1	0.207	0.207	0.261	RANDOM	59.7

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
x_dihedral_angle_d	23.4
x_scangle_it	6.44
x_mcangle_it	5.08
x_scbond_it	4.53
x_mcbond_it	3.18
x_improper_angle_d	2.47
x_angle_deg	1.6
x_bond_d	0.012
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7926
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	266

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing