9O5G | pdb_00009o5g

Room-temperature joint X-ray/Neutron structure of Thermus thermophilus SHMT in complex with PLP-Gly external aldimine and 5-methyl-tetrahydrofolate (5MTHF)

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

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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	50mM NaOAc, 0.5M Li2SO4, 1.0M Ammonium SO4

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.917	α = 90
b = 83.683	β = 91.64
c = 95.523	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	LADI III		2024-04-24	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M		2024-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL BEAMLINE LADI III	2.8-3.75	ILL	LADI III
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	2.1	50.7	76.6	0.224				0.989		6.3	5.2		40997
2	1.7	95.5	99.3	0.089				0.989		21.7	4.2		101159

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	2.1	2.21		0.495				0.718		2.5	5.5
2	1.7	1.76		0.487				0.667		1.8	3

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	2.1	36.58		2.5		36440	1901	67.5			0.292		0.327		random	19.2
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.7	29.45		2.5		91923	4528	90.2			0.181	0.3527	0.195	0.3603	random	19.2

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	17.9
x_torsion_deg	17.9
x_torsion_impr_deg	1.65
x_torsion_impr_deg	1.65
x_angle_deg	1
x_angle_deg	1
x_bond_d	0.007
x_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6220
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	78

Software

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