3KWK

Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (NP_809094.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.54 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.215	α = 90
b = 42.215	β = 90
c = 186.713	γ = 90

Symmetry
Space Group	P 43 21 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	MARMOSAIC 325 mm CCD	Flat mirror, vertical and horizontal focussing mirrors	2009-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.54	29.854	98.6	0.11	0.11	11	6.2		25905

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.58	87.5		0.55	0.55	1.4	3.1	1631

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.54	29.854	25811	1313	98.59	0.147	0.146	0.176	RANDOM	12.866

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]
0.03			0.03		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.2
r_dihedral_angle_4_deg	19.801
r_dihedral_angle_3_deg	12.52
r_scangle_it	6.297
r_dihedral_angle_1_deg	5.713
r_scbond_it	4.223
r_mcangle_it	2.379
r_angle_refined_deg	1.564
r_mcbond_it	1.454
r_angle_other_deg	0.919

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.2
r_dihedral_angle_4_deg	19.801
r_dihedral_angle_3_deg	12.52
r_scangle_it	6.297
r_dihedral_angle_1_deg	5.713
r_scbond_it	4.223
r_mcangle_it	2.379
r_angle_refined_deg	1.564
r_mcbond_it	1.454
r_angle_other_deg	0.919
r_mcbond_other	0.439
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1333
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	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.