3EH4 | pdb_00003eh4

Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.851	α = 90
b = 120.851	β = 90
c = 150.397	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	Q315R	ADSC Quantum-315R CCD	Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).	2007-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979	SSRL	BL7-1

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	2.6	20	99.5	0.041	7.9	4.1		34723	2	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)
1	2.6	2.67	100		0.678	0.9	4.4

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1XME	2.9	19.96	23877	1250	99.5	0.20169	0.19844	0.21	0.26762	RANDOM	105.967

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]
-0.48			-0.48		0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.582
r_dihedral_angle_3_deg	22.783
r_dihedral_angle_4_deg	21.203
r_dihedral_angle_1_deg	8.34
r_scangle_it	4.91
r_scbond_it	3.559
r_mcangle_it	3.03
r_angle_refined_deg	2.44
r_mcbond_it	1.809
r_symmetry_vdw_refined	0.386
r_nbtor_refined	0.33
r_nbd_refined	0.272
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.15
r_symmetry_hbond_refined	0.068
r_metal_ion_refined	0.053
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
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	5966
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	132

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling