1Y5N

The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q16

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	peg 3000, sodium acetate, potassium chloride, EDTA, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.26	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.258	α = 90
b = 241.957	β = 90
c = 140.121	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 210	KOHZU: Double Crystal Si(111)	2003-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0781	ALS	8.2.1

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	2.5	25	81.6	0.063	13.1	2.9	73777	73777	2		36.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	54.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1Q16	2.5	24.84	73659	73659	6007	81.4	0.19	0.19	0.238	RANDOM	50.7

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]
-6.39			24.4		-18.01

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.4
c_scangle_it	6.89
c_scbond_it	5.08
c_mcangle_it	4.64
c_mcbond_it	3.17
c_angle_deg	1.4
c_improper_angle_d	0.88
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15638
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	280

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing