3L5A

Crystal structure of a probable NADH-dependent flavin oxidoreductase from Staphylococcus aureus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	30% PEG200, 0.1M MES, 5mM I3C, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.941	α = 90
b = 75.342	β = 90
c = 80.736	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	CCD	MAR CCD 165 mm	Si(111) double-crystal monochromator	2009-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	0.97920	APS	17-BM

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	1.65	50	99.7	0.097	14.5	14.3		51898

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)
	1.65	1.69	96.5		0.405		11.4	3278

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	1.65	34.964	51815	2642	99.671	0.1812	0.1915	24.733

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]
0.022			-0.003		-0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.899
r_dihedral_angle_3_deg	12.968
r_dihedral_angle_4_deg	11.404
r_dihedral_angle_1_deg	5.658
r_scangle_it	3.618
r_scbond_it	2.173
r_mcangle_it	1.338
r_angle_refined_deg	1.252
r_mcbond_it	0.714
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.899
r_dihedral_angle_3_deg	12.968
r_dihedral_angle_4_deg	11.404
r_dihedral_angle_1_deg	5.658
r_scangle_it	3.618
r_scbond_it	2.173
r_mcangle_it	1.338
r_angle_refined_deg	1.252
r_mcbond_it	0.714
r_nbtor_refined	0.309
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.113
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2989
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.