3K7Q

Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K7M	PDB ENTRY 3K7M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.988	α = 90
b = 162.988	β = 90
c = 162.988	γ = 90

Symmetry
Space Group	P 4 3 2

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	MAR CCD 130 mm	KB-mirror	2001-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.782	ESRF	ID13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	20	100	0.109	0.109	22	11	47039	47039		2	31.38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.05	2.1	100		0.71	0.71	3.3	11	3282

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	MOLREP	THROUGHOUT	PDB ENTRY 3K7M	2.05	12.22	44283	44208	2343	99.83	0.20398	0.20159	0.24967	RANDOM	31.389

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.28
r_dihedral_angle_4_deg	20.192
r_dihedral_angle_3_deg	14.73
r_dihedral_angle_1_deg	6.8
r_scangle_it	6.425
r_scbond_it	4.292
r_angle_refined_deg	3.007
r_mcangle_it	2.75
r_mcbond_it	1.808
r_nbtor_refined	0.351

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.28
r_dihedral_angle_4_deg	20.192
r_dihedral_angle_3_deg	14.73
r_dihedral_angle_1_deg	6.8
r_scangle_it	6.425
r_scbond_it	4.292
r_angle_refined_deg	3.007
r_mcangle_it	2.75
r_mcbond_it	1.808
r_nbtor_refined	0.351
r_symmetry_vdw_refined	0.289
r_nbd_refined	0.279
r_symmetry_hbond_refined	0.261
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.201
r_bond_refined_d	0.032
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3323
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	109

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.