5GUW | pdb_00005guw

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O0R	3O0R, 1NIR
experimental model	PDB	1NIR	3O0R, 1NIR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	0.1M MES, 0.2M CsCl, 12% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.871	α = 90
b = 128.606	β = 106.83
c = 127.807	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX225HE	mirrors	2013-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	98.7	0.117	0.138	0.073	5.6	3.5		56669

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.31	98.2		0.647	0.659		3.3

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3O0R, 1NIR	3.2	49.48	47760	2551	87.67	0.2119	0.2097	0.21	0.254	0.25	RANDOM	67.021

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]
0.35		2.33	-1.92		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.32
r_dihedral_angle_4_deg	18.814
r_dihedral_angle_3_deg	17.242
r_dihedral_angle_1_deg	6.235
r_angle_refined_deg	1.546
r_angle_other_deg	0.889
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.32
r_dihedral_angle_4_deg	18.814
r_dihedral_angle_3_deg	17.242
r_dihedral_angle_1_deg	6.235
r_angle_refined_deg	1.546
r_angle_other_deg	0.889
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17804
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	549

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	phasing
HKL-2000	data reduction

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.