5XVK | pdb_00005xvk

Crystal structure of mouse Nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl Nicotinamide (MNA)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I62

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.25M Sodium thiocyanate, 22%(w/v) PEG 3350, 3% TMAO as additive

Crystal Properties
Matthews coefficient	Solvent content
2.27	41.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.138	α = 90
b = 71.699	β = 90
c = 157.042	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r		2016-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95370	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.88	78.57	99.7	0.102	0.107	0.035	0.998	15.2	9.5		44282

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.92	95.8		0.536	0.572	0.195	0.869		8.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2I62	1.88	78.57	41977	2233	99.69	0.1858	0.1843	0.18	0.2133	0.21	RANDOM	15.41

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]
-0.36			0.41		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.846
r_dihedral_angle_4_deg	15.731
r_dihedral_angle_3_deg	13.379
r_dihedral_angle_1_deg	5.467
r_angle_refined_deg	1.16
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.846
r_dihedral_angle_4_deg	15.731
r_dihedral_angle_3_deg	13.379
r_dihedral_angle_1_deg	5.467
r_angle_refined_deg	1.16
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4080
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	92

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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.