8SUJ

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)
TypeSourceAccession CodeDetails
experimental modelPDB 2DKJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.528940 mM NaOAc pH 5.5, 1.0 M (NH4)2SO4, and 0.5 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.6253.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.807α = 90
b = 83.334β = 91.68
c = 95.568γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron293IMAGE PLATEMAATEL IMAGINEelliptical mirrors2022-03-29LLAUE
21x-ray293PIXELDECTRIS EIGER R 4MOsmic VariMax2022-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1NUCLEAR REACTORORNL High Flux Isotope Reactor BEAMLINE CG4D2.8-4.5ORNL High Flux Isotope ReactorCG4D
2ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.347.7885.40.1610.080.9434.34.132586
2295.5499.90.0910.0440.99317.35.462364
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)RedundancyNumber Unique Reflections (All)
12.32.420.2810.1450.6372.93.8
222.070.3640.11770.8823.95.2

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.3402.531065155375.50.210.239random18.35
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2402.558902295494.40.1640.177random18.35
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
KeyRefinement Restraint Deviation
x_torsion_deg18
x_torsion_deg18
x_angle_deg1
x_angle_deg1
x_torsion_impr_deg0.79
x_torsion_impr_deg0.79
x_bond_d0.008
x_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6250
Nucleic Acid Atoms
Solvent Atoms429
Heterogen Atoms10

Software

Software
Software NamePurpose
nCNSrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
SCALAdata scaling
LAUEGENdata reduction