3PP8

2.1 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5). Screen solution: 0.2M Sodium acetate, 0.1M Bis-Tris (pH 6.5), 0.01M Glycolic acid, 30% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.495	α = 90
b = 139.371	β = 90
c = 111.043	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 225 mm CCD	Beryllium lenses	2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.1	30	99.9	0.074	39.3	6.1	18836	18836		-3	36

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)
	2.1	2.14	100		0.486	3.8	6.2	924

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3KBO	2.1	29.51	17835	17835	967	99.84	0.19865	0.19865	0.19659	0.23508	RANDOM	44.491

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]
-0.95			-0.72		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.6
r_dihedral_angle_4_deg	14.205
r_dihedral_angle_3_deg	13.422
r_scangle_it	4.972
r_scbond_it	3.565
r_dihedral_angle_1_deg	3.508
r_mcangle_it	2.144
r_angle_refined_deg	1.396
r_mcbond_it	1.314
r_angle_other_deg	0.816

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.6
r_dihedral_angle_4_deg	14.205
r_dihedral_angle_3_deg	13.422
r_scangle_it	4.972
r_scbond_it	3.565
r_dihedral_angle_1_deg	3.508
r_mcangle_it	2.144
r_angle_refined_deg	1.396
r_mcbond_it	1.314
r_angle_other_deg	0.816
r_mcbond_other	0.41
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2449
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

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.