2REH

Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C0U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	24-26% PEG 3350, 30% glycerol, 0.1M Na Cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	58.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.934	α = 90
b = 108.934	β = 90
c = 337.671	γ = 120

Symmetry
Space Group	P 32 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 315		2007-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	2.4	50	88.2	0.081	22.3	4.1		81048

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)
	2.4	2.49	53.7		0.414	1.27	2.2	4878

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	2c0u	2.4	50	76997	4051	88.09	0.20657	0.20364	0.2633	RANDOM	44.049

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]
-0.05	-0.03		-0.05		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.337
r_dihedral_angle_4_deg	21.334
r_dihedral_angle_3_deg	19.1
r_dihedral_angle_1_deg	7.097
r_scangle_it	3.871
r_scbond_it	2.518
r_angle_refined_deg	2.025
r_mcangle_it	1.565
r_mcbond_it	1.007
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.337
r_dihedral_angle_4_deg	21.334
r_dihedral_angle_3_deg	19.1
r_dihedral_angle_1_deg	7.097
r_scangle_it	3.871
r_scbond_it	2.518
r_angle_refined_deg	2.025
r_mcangle_it	1.565
r_mcbond_it	1.007
r_nbtor_refined	0.308
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.207
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.137
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13204
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	212

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

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.