9DSW | pdb_00009dsw

Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with L-threonine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9DG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	14% PEG8000, 20% glycerol, 150 mM calcium acetate, 80 mM sodium cacodylate, pH 6.5, 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 1 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.86	68.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.672	α = 90
b = 153.672	β = 90
c = 86.733	γ = 120

Symmetry
Space Group	P 31 2 1

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 2M		2023-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.19499	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.05	44.5	99.9	0.244	0.247	0.04	0.999	16	35.3		73986

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09			0.87	0.247	0.04	0.366

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.05	44.4	64297	3283	91.17	0.18993	0.18932	0.1982	0.20183	0.2039	RANDOM	31.737

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]
0.18	0.09		0.18		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.893
r_dihedral_angle_2_deg	9.391
r_long_range_B_refined	7.606
r_long_range_B_other	7.605
r_dihedral_angle_1_deg	6.776
r_scangle_other	5.547
r_mcangle_it	3.998
r_mcangle_other	3.997
r_scbond_it	3.357
r_scbond_other	3.356
r_mcbond_it	2.486
r_mcbond_other	2.481
r_angle_refined_deg	1.389
r_angle_other_deg	0.464
r_chiral_restr	0.067
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_gen_planes_refined
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5144
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing