5J62

FMN-dependent Nitroreductase (CDR20291_0684) from Clostridium difficile R20291

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PXV	ensemble model of 3PXV and 3EK3
experimental model	PDB	3EK3	ensemble model of 3PXV and 3EK3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	0.1 M sodium citrate, pH 5.6 10% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.323	α = 90
b = 100.323	β = 90
c = 99.921	γ = 90

Symmetry
Space Group	P 41 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		2015-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.98	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.15	50	100	0.076	0.078	0.016	6.6	23.9		28386

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	99.9		0.742	0.775	0.218	0.816		11.9	1388

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	ensemble model of 3PXV and 3EK3	2.15	35.47	26891	1415	99.81	0.1698	0.1673	0.2175	RANDOM	45.286

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]
0.23			0.23		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.896
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_4_deg	8.659
r_dihedral_angle_1_deg	5.865
r_mcangle_it	5.489
r_mcbond_it	3.998
r_mcbond_other	3.975
r_angle_refined_deg	1.766
r_angle_other_deg	1.041
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.896
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_4_deg	8.659
r_dihedral_angle_1_deg	5.865
r_mcangle_it	5.489
r_mcbond_it	3.998
r_mcbond_other	3.975
r_angle_refined_deg	1.766
r_angle_other_deg	1.041
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3259
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	phasing
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

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.