21JX | pdb_000021jx

Crystal structure of compound 1 bound to human Nicotinamide N-methyltransferase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.582	α = 90
b = 98.826	β = 90
c = 72.821	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	RIGAKU RAXIS IV++		2017-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.34	72.82	99.9	0.135	11.3	3.7		38539

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.42			0.471

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.34	72.82	36592	1915	99.78	0.20225	0.19849	0.2001	0.27321	0.2747	RANDOM	36.472

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]
0.01		-0.01	-0.03		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.21
r_dihedral_angle_3_deg	19.057
r_dihedral_angle_4_deg	18.439
r_long_range_B_refined	7.332
r_dihedral_angle_1_deg	7.184
r_mcangle_it	4.323
r_scbond_it	3.346
r_mcbond_it	2.828
r_angle_refined_deg	1.784
r_chiral_restr	0.117
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7909
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	88

Software

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