2Q4D

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.589	α = 90
b = 80.427	β = 102.97
c = 50.709	γ = 90

Symmetry
Space Group	C 1 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			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 1YDH	2.152	34.35	25678	1300	99	0.152	0.152	0.207	RANDOM	26.5

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]
1.08		1.17			-1.07

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.3
c_scangle_it	2.57
c_scbond_it	1.96
c_mcangle_it	1.73
c_mcbond_it	1.2
c_angle_deg	1.1
c_improper_angle_d	0.83
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2796
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	20

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.