Experiment: 6SMR

A. thaliana serine hydroxymethyltransferase isoform 4 (AtSHMT4) in complex with methotrexate

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	8.2	292	Crystals grew in 80 mM Tris-HCl pH 8.2, 20% PEG3350. Mature crystals were transferred to drops with 80 mM Tris-HCl pH 8.2, 20% PEG3350, 20% ethylene glycol, 50 mM L-serine, and 10 mM MTX. After 24-h incubation, crystals were harvested and vitrified in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.856	α = 90
b = 120.975	β = 90
c = 131.8	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	PIXEL	DECTRIS EIGER X 16M		2018-06-27	M	SINGLE WAVELENGTH

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

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	2.12	90	98.8	0.095	0.108	1	11.6	4.2		106878

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	2.12	2.25	98.7		0.666	0.76	0.79	1.9	4.3

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	2.12	88.3	105720	1068	98.8	0.1738	0.1732	0.1826	0.234	0.2414	random	38.9

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	0.898
bonds	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14583
Nucleic Acid Atoms
Solvent Atoms	965
Heterogen Atoms	231

Software

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