Experiment: 9BOW

X-ray structure of Thermus thermophilus serine hydroxymethyltransferase with PLP-L-Ser external aldimine and 5-formyltetrahydrofolate (folinic acid)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SUJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289.15	40 mM NaOAc pH 5.5, 1 M (NH4)2SO4, 0.5 M Li2SO4, soaked in 40 mM NaOAc pH 5.5, 0.5 M L-Ser, 15% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.131	α = 90
b = 82.814	β = 91.58
c = 94.446	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	293	PIXEL	DECTRIS EIGER R 4M	Osmic VariMax	2023-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5406

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.8	29.05	92.2	0.03	0.026	0.997	23.3	3.5		76390

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	56.4		0.111	0.105	0.969	7.6	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	29.05	1.07	76265	3838	91.98	0.1329	0.1315	0.1332	0.1595	0.1574

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
f_dihedral_angle_d	13.069
f_angle_d	1.245
f_chiral_restr	0.084
f_plane_restr	0.018
f_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6233
Nucleic Acid Atoms
Solvent Atoms	826
Heterogen Atoms	73

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
CrysalisPro	data reduction
PHASER	phasing