3QJR | pdb_00003qjr

The structure of and photolytic induced changes of carbon monoxide binding to the 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	PDB entry 1XME

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	7% PEK 2K, 50 mM KCl, 20 mM Bis-Tris pH 7.0, 6.5 mM n-nonyl-beta-D-glucopyranoside , VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.81	α = 90
b = 108.81	β = 90
c = 164.46	γ = 90

Symmetry
Space Group	P 43 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	CCD	MARMOSAIC 325 mm CCD		2010-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	3.2	76.94	96.6	0.06	5.2	5.4	16200	16200

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	3.2	3.37	97.6		0.385	2	6.9	2339

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 entry 1XME	3.2	19.89	16200	14475	778	90.64	0.32062	0.32062	0.3183	0.31	0.36668	0.35	RANDOM	23.728

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]
2.21			2.21		-4.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.451
r_dihedral_angle_4_deg	20.422
r_dihedral_angle_3_deg	16.936
r_dihedral_angle_1_deg	5.185
r_angle_refined_deg	1.488
r_scangle_it	0.762
r_scbond_it	0.45
r_mcangle_it	0.232
r_mcbond_it	0.111
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.451
r_dihedral_angle_4_deg	20.422
r_dihedral_angle_3_deg	16.936
r_dihedral_angle_1_deg	5.185
r_angle_refined_deg	1.488
r_scangle_it	0.762
r_scbond_it	0.45
r_mcangle_it	0.232
r_mcbond_it	0.111
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5924
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	113

Software

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

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.