3EHB

A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AR1	PDB ENTRY 1AR1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	291	MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.1	70.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.461	α = 90
b = 151.332	β = 90
c = 157.487	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 225 mm CCD		2006-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.92021	SLS	X10SA

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	2.32	20	98.8	0.09	19.14		87146	87146	-3	-3	51.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.32	2.4	97		3.93		8161

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1AR1	2.32	19.69	-3	86853	84230	2623	100	0.20618	0.20618	0.20505	0.2424	RANDOM	60.153

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
r_dihedral_angle_2_deg	37.705
r_dihedral_angle_4_deg	25.498
r_dihedral_angle_3_deg	19.058
r_dihedral_angle_1_deg	7.709
r_mcangle_it	5.882
r_scangle_it	5.773
r_mcbond_it	4.385
r_scbond_it	4.243
r_angle_refined_deg	2.488
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.197
r_metal_ion_refined	0.184
r_chiral_restr	0.182
r_symmetry_hbond_refined	0.05
r_bond_refined_d	0.027
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7954
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	703

Software

Software
Software Name	Purpose
SBC-Collect	data collection
DM	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
DM	phasing