Experiment: 3R3S

Structure of the YghA Oxidoreductase from Salmonella enterica

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I3O	PDB ENTRY 3I3O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	2 M ammonium sulfate, 100 mM Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.728	α = 90
b = 80.673	β = 100.96
c = 96.168	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	110	CCD	MARMOSAIC 300 mm CCD	beryllium lens	2010-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G		APS	21-ID-G

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	1.25	50	99.3	0.107	14.8	5.8	313957	311759	1.5	2	8.2

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)
	1.25	1.29	95.3		0.527	2.2	3.6	29843

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 3I3O	1.25	27.34	2.2	1.44	314700	311679	15585	99	0.13	0.129	0.1259	0.153	0.1503	RANDOM	11.78

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]
3.46		1.35	0.84		0.32

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.396
f_angle_d	1.546
f_chiral_restr	0.095
f_bond_d	0.012
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8788
Nucleic Acid Atoms
Solvent Atoms	1943
Heterogen Atoms	197

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MrBUMP/MolRep	phasing