7WAR | pdb_00007war

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

X-RAY DIFFRACTION

---

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
2.71	54.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.7	α = 90
b = 96.7	β = 90
c = 166.9	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	2.101	19.712	99.8	0.218	0.238	0.094	0.891	9.2	6.4		53180			31.43

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	2.101	2.14	99		0.724	0.788	0.31	0.79	2	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	2.101	19.712	53133	2652	99.67	0.172	0.1708	0.18	0.2025	0.21	34.983

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]
-0.495	-0.248		-0.495		1.606

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.335
r_dihedral_angle_3_deg	16.121
r_dihedral_angle_2_deg	12.256
r_lrange_other	10.505
r_lrange_it	10.501
r_scangle_it	8.856
r_scangle_other	8.855
r_dihedral_angle_1_deg	7.28
r_scbond_it	6.298
r_scbond_other	6.297
r_mcangle_it	5.995
r_mcangle_other	5.995
r_mcbond_it	4.498
r_mcbond_other	4.495
r_angle_refined_deg	2.023
r_angle_other_deg	0.677
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_other	0.235
r_nbd_refined	0.223
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_other	0.173
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5616
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	274

Software

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