2Q41

Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820

X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.814	α = 90
b = 95.207	β = 104.96
c = 89.164	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			APS-1			M	SINGLE WAVELENGTH

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Re-refinement using ensemble model	THROUGHOUT	PDB entry 1XJ5	2.7	26.29	37779	3788	95.5	0.164	0.164	0.249	RANDOM	37.2

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]
-2.91		1.24	14.18		-11.27

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.6
c_scangle_it	5.02
c_mcangle_it	3.87
c_scbond_it	3.12
c_mcbond_it	2.19
c_angle_deg	1.3
c_improper_angle_d	0.95
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8864
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.