3PXV

Crystal structure of a Nitroreductase with bound FMN (Dhaf_2018) from Desulfitobacterium hafniense DCB-2 at 2.30 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	20.00% polyethylene glycol 3350, 0.20M ammonium dihydrogen phosphate, No Buffer pH 4.6, 0.001 M flavin mononucleotide (FMN), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.261	α = 90
b = 81.577	β = 90
c = 161.754	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	MARMOSAIC 325 mm CCD		2010-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	28.73	99.5	0.143	6.8	4.6	36709	36709			34.74

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	2.3	2.36	96.2		0.666	0.666	1.8	3.6	2593

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	2.3	28.73	36660	1833	99.57	0.1773	0.1743	0.2352	RANDOM	51.0065

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]
0.01			0.34		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.413
r_dihedral_angle_3_deg	13.53
r_dihedral_angle_4_deg	11.811
r_scangle_it	6.693
r_scbond_it	4.666
r_dihedral_angle_1_deg	3.119
r_mcangle_it	2.626
r_angle_refined_deg	1.518
r_mcbond_it	1.417
r_angle_other_deg	0.949

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.413
r_dihedral_angle_3_deg	13.53
r_dihedral_angle_4_deg	11.811
r_scangle_it	6.693
r_scbond_it	4.666
r_dihedral_angle_1_deg	3.119
r_mcangle_it	2.626
r_angle_refined_deg	1.518
r_mcbond_it	1.417
r_angle_other_deg	0.949
r_mcbond_other	0.504
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5694
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	124

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.