7WAS | pdb_00007was

SbSOMT in complex with pterostilbene and nicotinamide adenine dinucleotide(NAD+)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	0.1 M sodium acetate pH 4.6, 0.2 M sodium acetate , 0.2 M ammonium chloride, 2.5% (w/v) polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.469	α = 90
b = 96.469	β = 90
c = 169.43	γ = 120

Symmetry
Space Group	P 31 2 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	PIXEL	PSI PILATUS 6M		2021-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9784	SSRF	BL19U1

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	2.401	31.421	99.8	0.199	0.204	0.046	0.915	7.5	19.5		36363			36.78

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	2.401	2.44	99.9		0.955	0.982	0.228	0.871	0.8	6.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7vb8	2.401	31.421	36012	1899	99.138	0.19	0.1873	0.19	0.2462	0.25	43.738

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]
-0.756	-0.378		-0.756		2.451

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.674
r_dihedral_angle_6_deg	15.666
r_dihedral_angle_2_deg	13.217
r_lrange_other	12.921
r_lrange_it	12.92
r_scangle_it	10.395
r_scangle_other	10.393
r_mcangle_it	8.495
r_mcangle_other	8.494
r_dihedral_angle_1_deg	7.863
r_scbond_it	7.747
r_scbond_other	7.745
r_mcbond_other	6.149
r_mcbond_it	6.148
r_angle_refined_deg	1.993
r_angle_other_deg	0.651
r_symmetry_xyhbond_nbd_other	0.257
r_nbd_other	0.25
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.215
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.179
r_ncsr_local_group_1	0.129
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_refined	0.077
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5622
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	214

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing