Experiment: 4U9G

Crystal structure of an H-NOX protein from S. oneidensis in the Fe(II)CO ligation state, Q154A/Q155A/K156A mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4U99

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 CARBON MONOXIDE-SATURATED CRYOPROTECTANT FOR 15-45 MINUTES. CRYSTAL GROWTH AND MANIPULATION WAS PERFORMED ANAEROBICALLY.

Crystal Properties
Matthews coefficient	Solvent content
4.59	73.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.173	α = 90
b = 164.173	β = 90
c = 102.366	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		2014-01-09	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	2.25	43.007	96.7	0.028	20.2	11.1		70856

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	2.25	2.32	98.1		0.446	1.8	11.1

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	4U99	2.25	43.01	1.34	70856	3571	96.7	0.182	0.182	0.1976	0.193	0.2047

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	14.513
f_angle_d	0.887
f_chiral_restr	0.028
f_bond_d	0.009
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2951
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	91

Software

Software
Software Name	Purpose
PHENIX	refinement