3K7M | pdb_00003k7m

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	20mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.919	α = 90
b = 163.92	β = 90
c = 163.919	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 165 mm	mirrors	2000-09-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2000-09-24	M	MAD
3	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2000-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6
2	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05, 0.9185, 0.9207, 0.900	MPG/DESY, HAMBURG	BW6
3	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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
1,2,3	1.95	20	99.6	0.059	0.059	28.9	15	55137	54917		2	33.3

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)
	1.95	2	94.3		0.623	0.623	3	7.5	3615

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.95	14.4	52074	51689	2762	99.26	0.17796	0.17607	0.19	0.2134	0.22	RANDOM	33.324

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	37.248
r_dihedral_angle_4_deg	19.025
r_dihedral_angle_3_deg	14.595
r_dihedral_angle_1_deg	6.506
r_scangle_it	6.281
r_scbond_it	4.411
r_angle_refined_deg	2.63
r_mcangle_it	2.603
r_mcbond_it	1.863
r_nbtor_refined	0.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.248
r_dihedral_angle_4_deg	19.025
r_dihedral_angle_3_deg	14.595
r_dihedral_angle_1_deg	6.506
r_scangle_it	6.281
r_scbond_it	4.411
r_angle_refined_deg	2.63
r_mcangle_it	2.603
r_mcbond_it	1.863
r_nbtor_refined	0.327
r_symmetry_vdw_refined	0.324
r_symmetry_hbond_refined	0.278
r_chiral_restr	0.238
r_xyhbond_nbd_refined	0.236
r_nbd_refined	0.229
r_bond_refined_d	0.035
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3334
Nucleic Acid Atoms
Solvent Atoms	618
Heterogen Atoms	96

Software

Software
Software Name	Purpose
MAR345	data collection
SHELXS	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.