5XVQ | pdb_00005xvq

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

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	295	0.1M MES pH 6.2, 23%(w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.071	α = 90
b = 65.028	β = 89.97
c = 91.144	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	VariMax HR Optics	2017-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.29	91.29	95.4	0.177	0.202	0.096	5.7	4		21145

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	2.29	2.38	98.1		0.108	0.123	0.056	0.986		4.4

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	3ROD	2.29	91.29	20046	1085	95.05	0.1972	0.1938	0.1929	0.2615	0.2608	RANDOM	25.205

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]
-0.99		-0.2	-0.46		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.181
r_dihedral_angle_4_deg	19.357
r_dihedral_angle_3_deg	17.085
r_dihedral_angle_1_deg	6.261
r_angle_refined_deg	1.249
r_nbtor_refined	0.3
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.156
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3986
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	84

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing