8SUJ | pdb_00008suj

Joint X-ray/neutron structure of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in internal aldimine state

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DKJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	40 mM NaOAc pH 5.5, 1.0 M (NH4)2SO4, and 0.5 M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.807	α = 90
b = 83.334	β = 91.68
c = 95.568	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	neutron	293	IMAGE PLATE	MAATEL IMAGINE	elliptical mirrors	2022-03-29	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M	Osmic VariMax	2022-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ORNL High Flux Isotope Reactor BEAMLINE CG4D	2.8-4.5	ORNL High Flux Isotope Reactor	CG4D
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	2.3	47.78	85.4	0.161			0.08	0.943		4.3	4.1		32586
2	2	95.54	99.9	0.091			0.044	0.993		17.3	5.4		62364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42		0.281			0.145	0.637		2.9	3.8
2	2	2.07		0.364			0.1177	0.882		3.9	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.3	40		2.5		31065	1553	75.5			0.21		0.239		random	18.35
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2	40		2.5		58902	2954	94.4			0.164	0.34	0.177	0.33	random	18.35

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
x_torsion_deg	18
x_torsion_deg	18
x_angle_deg	1
x_angle_deg	1
x_torsion_impr_deg	0.79
x_torsion_impr_deg	0.79
x_bond_d	0.008
x_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6250
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms	10

Software

Software
Software Name	Purpose
nCNS	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing
SCALA	data scaling
LAUEGEN	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.