7VB8 | pdb_00007vb8

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		MrBUMP generated chimeric model

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	55.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.831	α = 90
b = 96.831	β = 90
c = 168.038	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		2020-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97853	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	1.72	48.462	99.8	0.06	0.063	0.02	1	30.2	19.4		97225			22.6

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	1.72	1.75	97.1		0.941	1.01	0.357	0.849	2.9	14.6

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	MrBUMP generated chimeric model	1.72	48.462	97159	4899	99.826	0.165	0.1633	0.18	0.1893	0.2	26.372

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]
-0.735	-0.367		-0.735		2.383

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.817
r_dihedral_angle_6_deg	15.67
r_dihedral_angle_3_deg	14.638
r_lrange_it	8.15
r_lrange_other	8.107
r_dihedral_angle_1_deg	6.362
r_scangle_it	6.057
r_scangle_other	6.057
r_scbond_it	4.125
r_scbond_other	4.125
r_mcangle_it	3.93
r_mcangle_other	3.929
r_mcbond_it	2.816
r_mcbond_other	2.816
r_angle_refined_deg	1.639
r_angle_other_deg	0.558
r_nbd_refined	0.225
r_nbd_other	0.217
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.176
r_symmetry_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.164
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5622
Nucleic Acid Atoms
Solvent Atoms	568
Heterogen Atoms	229

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	phasing