4U9K | pdb_00004u9k

Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II)NO ligation state, Q154A/Q155A/K156A mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4U9J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	293	OBTAINED BY EQUILIBRATING A 2 UL DROP OF 1:1 PROTEIN:RESERVOIR AGAINST A 700 UL RESERVOIR CONTAINING 1.6-1.9 M DL-MALIC ACID (PH 7.3). FOR CRYOPROTECTION, 2 UL OF MOTHER LIQUOR CONTAINING 10% GLYCEROL WAS ADDED DIRECTLY TO THE DROP AND CRYSTALS WERE SERIAL TRANSFERRED INTO MOTHER LIQUOR SOLUTION CONTAINING 5, 7.5 AND 10% GLYCEROL. PRIOR TO FLASH FREEZING IN LIQUID NITROGEN, CRYSTALS WERE TRANSFERRED UNDER A LAYER OF OIL AND INCUBATED WITH ANAEROBIC CRYOPROTECTANT CONTAINING APPROXIMATELY 0.001 M NITRIC OXIDE FOR 15-45 MINUTES. CRYSTAL GROWTH AND MANIPULATION WAS PERFORMED ANAEROBICALLY.

Crystal Properties
Matthews coefficient	Solvent content
4.57	73.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.303	α = 90
b = 164.303	β = 90
c = 101.679	γ = 120

Symmetry
Space Group	P 63 2 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	ADSC QUANTUM 315r		2013-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.00	ALS	8.2.1

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	2.45	47.875	99.77	0.032	19.3	10.7	56342	56342

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	2.45	2.55	100		0.663	1.6	11

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	FREE R-VALUE	4U9J	2.45	47.875	1.34	56342	2848	99.77	0.1835	0.1822	0.19	0.2069	0.22

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.738
f_angle_d	1.643
f_chiral_restr	0.176
f_bond_d	0.022
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2951
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	91

Software

Software
Software Name	Purpose
PHENIX	refinement

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.