3O5A

Crystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus necator using Ionic Liquids

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NAP	PDB ENTRY 2NAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	15% PEG 3350, 0.2M sodium formate, 0.4M [C4MIM]Cl-, pH 7.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.4	α = 90
b = 71.41	β = 121.04
c = 128.41	γ = 90

Symmetry
Space Group	C 1 2 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		2007-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.72	28.34	99.6174		3.5	130188	97895	4	935

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.81	99.6174

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NAP	1.72	27.63	154350	93004	4889	99.62	0.1435	0.14473	0.14278	0.1815	RANDOM	12.375

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]
-0.09		-0.04	0.07		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.44
r_dihedral_angle_4_deg	18.611
r_dihedral_angle_3_deg	13.8
r_dihedral_angle_1_deg	8.731
r_scangle_it	4.383
r_scbond_it	2.971
r_angle_refined_deg	2.31
r_mcangle_it	1.936
r_mcbond_it	1.289
r_chiral_restr	0.198

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.44
r_dihedral_angle_4_deg	18.611
r_dihedral_angle_3_deg	13.8
r_dihedral_angle_1_deg	8.731
r_scangle_it	4.383
r_scbond_it	2.971
r_angle_refined_deg	2.31
r_mcangle_it	1.936
r_mcbond_it	1.289
r_chiral_restr	0.198
r_bond_refined_d	0.028
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7121
Nucleic Acid Atoms
Solvent Atoms	787
Heterogen Atoms	248

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.