9DSQ | pdb_00009dsq

Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with products TC-AMP and pyrophosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q9WZV6-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	294.15	Reservoir solution: 500 ul 80 mM sodium cacodylate, pH 7.4, 0.23 M sodium acetate, 13.5% PEG8000, 20% glycerol. Protein: 25 mg/mL TmTsaC2, 50 mM Tris, pH 7.5, 50 mM KCl, 1 mM DTT, 10 mM L-threonine, 30 mM sodium bicarbonate. Crystal soaked in 14% PEG8000, 20% glycerol, 0.2 M sodium acetate, 80 mM sodium cacodylate, pH 7.4, 10 mM L-threonine, 10 mM ATP, 10 mM MgCl2, 30 mM bicarbonate, 0.11 u/ul inorganic pyrophosphatase

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.825	α = 90
b = 153.825	β = 90
c = 86.892	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	80	PIXEL	DECTRIS PILATUS 6M		2024-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00004	ALS	5.0.2

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	1.99	44.44	100	0.271	0.279	0.064	0.997	7.9	18.6		81174

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	1.99	2.03	100		5.124	5.263	1.197	0.322	0.7

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	1.99	44.44	76961	4176	99.97	0.19828	0.19695	0.207	0.2225	0.2117	RANDOM	48.036

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]
0.98	0.49		0.98		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.792
r_long_range_B_refined	10.299
r_long_range_B_other	10.294
r_dihedral_angle_2_deg	9.156
r_scangle_other	8.284
r_dihedral_angle_1_deg	6.616
r_mcangle_it	6.01
r_mcangle_other	6.01
r_scbond_it	5.492
r_scbond_other	5.491
r_mcbond_it	4.187
r_mcbond_other	4.172
r_angle_refined_deg	1.261
r_angle_other_deg	0.432
r_chiral_restr	0.06
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	5123
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
REFMAC	phasing