Experiment: 7TA9

Crystal Structure of thymidylate synthase from Acinetobacter baumannii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IX6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	290	Protein at 34 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, and pentaethyleneglycol, and 0.1 M MES/imidazole pH 6.5 (Morpheus E1). Cryo: Direct. Tray: 320511e1: pin: jjg2-4.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.94	α = 90
b = 73.76	β = 90
c = 109.38	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 PILATUS3 6M	Beryllium Lenses	2021-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97740	ALS	5.0.1

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	1.5	44.52	98.6	0.035	0.038	1	38.92	8.388		83501			18.5

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	1.5	1.54	88.9		0.56	0.609	0.884	3.91	5.692

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ix6	1.5	44.52	1.34	83491	2026	98.56	0.1631	0.1624	0.162	0.1912	0.1914	25.6334

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4273
Nucleic Acid Atoms
Solvent Atoms	585
Heterogen Atoms	32

Software

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