1YKI

The structure of E. coli nitroreductase bound with the antibiotic nitrofurazone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ICU	pdb entry 1ICU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	291	PEG4000, ethylene glycol, nicotinic acid, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.078	α = 90
b = 56.466	β = 103.1
c = 116.085	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 4		2001-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	1.7	40	99.6	0.056	8.9	6.5	97110	97110			17.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.79	99.5		0.118	5.8	4.6	14083

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	pdb entry 1ICU	1.7	40	92255	4855	99.58	0.1449	0.14373	0.16685	RANDOM	11.066

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]
-0.29		0.04	0.29		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.363
r_scangle_it	2.604
r_scbond_it	1.597
r_angle_refined_deg	1.266
r_mcangle_it	0.918
r_angle_other_deg	0.804
r_mcbond_it	0.486
r_nbd_other	0.242
r_symmetry_vdw_other	0.232
r_symmetry_vdw_refined	0.216
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.194
r_xyhbond_nbd_refined	0.161
r_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6724
Nucleic Acid Atoms
Solvent Atoms	902
Heterogen Atoms	205

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing