3NK0 | pdb_00003nk0

Complex of 6-hydroxy-L-nicotine oxidase with inhibitor bound at active site and turnover product at exit cavity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K7M	PDB code 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
3.87	68.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.677	α = 90
b = 163.677	β = 90
c = 163.677	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	mirror	2003-03-17	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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.15	20	99.4	0.1	14	4.5	41095	40984		2	33.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	99.6		0.718	2	4.5	2023

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 3K7M	2.15	14.4	39048	38825	2054	99.43	0.16648	0.16422	0.18	0.21043	0.22	RANDOM	33.234

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	38.333
r_dihedral_angle_4_deg	19.168
r_dihedral_angle_3_deg	15.776
r_dihedral_angle_1_deg	7.309
r_scangle_it	5.785
r_scbond_it	3.825
r_mcangle_it	2.377
r_angle_refined_deg	2.269
r_mcbond_it	1.531
r_nbtor_refined	0.326
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.228
r_symmetry_hbond_refined	0.227
r_symmetry_vdw_refined	0.222
r_chiral_restr	0.187
r_bond_refined_d	0.029
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3272
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	123

Software

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