1OAH | pdb_00001oah

Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		15% W/V PEG 3350, CACL2 0.2M, HEPES PH7.5, 0.1M, 3-(DECYL-METHYLAMMONIUM)PROPANE-1-SULFONATE (ZWITTERGENT 3-10) AS ADDITIVE, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.34	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.94	α = 90
b = 104.6	β = 90
c = 143.18	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	IMAGE PLATE	MARRESEARCH		1999-05-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.7403,1.7390,0.9919, 0.932	ESRF	ID14-4

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	2.3	84.5	94	0.08	11.7	5.6		53690		2	30

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	2.3	2.38	89.8		0.39	2.2	4.9

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD AND MR	THROUGHOUT	PDB ENTRY 1QDB	2.3	20	51633	522	97.3	0.189	0.19	0.224	0.23	RANDOM	27.7

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]
1.28			1.03		-2.31

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7705
Nucleic Acid Atoms
Solvent Atoms	499
Heterogen Atoms	440

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHARP	phasing
AMoRE	phasing

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.