3NG7 | pdb_00003ng7

Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity

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	298	20mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.771	α = 90
b = 163.771	β = 90
c = 163.771	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	2003-03-21	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	1.95	20	99.6	0.1	15	5	55164	54943		2	25.95

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	1.95	1.97	96		0.702	2	4.5	2733

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	Molrep	THROUGHOUT	PDB ENTRY 3K7M	1.95	14.4	54943	51749	2766	99.58	0.16901	0.16715	0.19	0.20385	0.21	RANDOM	27.643

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	37.188
r_dihedral_angle_4_deg	18.4
r_dihedral_angle_3_deg	15.573
r_dihedral_angle_1_deg	7.072
r_scangle_it	6.434
r_scbond_it	4.382
r_mcangle_it	2.606
r_angle_refined_deg	2.542
r_mcbond_it	1.764
r_nbtor_refined	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.188
r_dihedral_angle_4_deg	18.4
r_dihedral_angle_3_deg	15.573
r_dihedral_angle_1_deg	7.072
r_scangle_it	6.434
r_scbond_it	4.382
r_mcangle_it	2.606
r_angle_refined_deg	2.542
r_mcbond_it	1.764
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.239
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.23
r_chiral_restr	0.226
r_xyhbond_nbd_refined	0.224
r_bond_refined_d	0.033
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3292
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	122

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.