Experiment: 6SMW

A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with pemetrexed

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	The AtSHMT2 crystals were grown by vapor diffusion method in hanging drops containing 3 uL of the protein solution and 2 uL of reservoir solution. The reservoir solution was composed of 90% Hampton Research Index F8 condition (0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, and 25% polyethylene glycol 3350). Mature crystals were transferred to drops with the original screen conditions supplemented with 20% ethylene glycol, 50 mM L-serine, and 10 mM PTX. After 24-h incubation, crystals were harvested and vitrified in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.899	α = 90
b = 130.288	β = 90
c = 150.777	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300-HS		2018-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.54	80	99.7	0.082	0.088	1	18.9	8.1		330027

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.64	98.2		1.25	1.34	0.67	1.8	7.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6cd0	1.54	80	328680	1320	99.7	0.1289	0.1287	0.1314	0.1662	0.1672	random

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]

RMS Deviations
Key	Refinement Restraint Deviation
angles	0.789
bonds	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14937
Nucleic Acid Atoms
Solvent Atoms	1936
Heterogen Atoms	333

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing