3R5W | pdb_00003r5w

Structure of Ddn, the Deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824, with co-factor F420

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R5R	PDB entry 3R5R (preliminary model)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	3.6 M Na-formate, 10% glycerol with equimolar protein and F420, pH 8.5, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.336	α = 90
b = 89.419	β = 96.29
c = 127.678	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315r		2009-07-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2009-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.979	ALS	5.0.2
2	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.979	ALS	5.0.2

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	1.786	50	97.5	0.073	22.9	3.1	174250	174250

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)
1,2	1.786	1.86	96.3		0.722	1.6	3.2	17150

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 3R5R (preliminary model)	1.786	42.169	0.08	159399	159341	7913	88.14	0.175	0.1733	0.18	0.2064	0.21	random	31.0082

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]
-0.5771		-2.9673	0.4187		0.1584

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.058
f_angle_d	1.568
f_chiral_restr	0.103
f_bond_d	0.013
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8740
Nucleic Acid Atoms
Solvent Atoms	1280
Heterogen Atoms	530

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
HKL-2000	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 R01GM157729.