6QWG | pdb_00006qwg

Serial Femtosecond Crystallography Structure of Cu Nitrite Reductase from Achromobacter cycloclastes: Nitrite complex at Room Temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.5	293	20 mg per ml AcNiR in 20 mM Tris HCl pH 7.5 mixed with 2.5 M ammonium sulfate, 0.1 M sodium citrate pH 4.5 in a ratio of 1 to 3 and mixed by vortexing for 60sec

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.6	α = 90
b = 97.6	β = 90
c = 97.6	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	301	CCD	MPCCD		2017-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.23	SACLA	BL2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (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	1.9	43.65	99.9	0.99	0.0973		3281		24729

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.968	99.8		0.63	0.586

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6GB8	1.9	43.648	1.34	24698	1001	99.98	0.1382	0.1368	0.1368	0.1723	0.172	37.1104

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2574
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	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.