9DG5 | pdb_00009dg5

Thermotoga maritima threonylcarbamoyl adenylate synthase (TsaC2) in complex with L-threonine, magnesium and ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9D3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	294.15	Reservoir solution: 80 mM sodium cacodylate, 110-160 mM calcium acetate, 14% PEG8000, 20% glycerol, final pH 6.2. Sample: 25 mg/ml TmTsaC2, 50 mM Tris (pH 7.5), 50 mM KCl and 1 mM DTT, 10 mM L-threonine, 1 mM AMPCPP and 1 mM MgCl2. Drop: 1.5 reservoir + 1.5 ul sample. Crystal soaked 10 min in 40% glycerol, 14.4% PEG8000, 80 mM sodium cacodylate, 160 mM sodium acetate, 10 mM L-threonine, 10 mM ATP, 10 mM MgCl2, 10 mM NaHCO3, pH 6.2

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.764	α = 90
b = 153.764	β = 90
c = 87.207	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		2024-02-22	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)	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	2.25	44.43	99.9	0.556	0.124	0.953	6.61	19.6		56743

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29			1.806	0.446	0.884

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	2.25	44.43	45571	2356	84.44	0.18493	0.18316	0.193	0.21894	0.2224	RANDOM	47.368

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]
-0.03	-0.01		-0.03		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.693
r_dihedral_angle_4_deg	19.716
r_dihedral_angle_3_deg	18.167
r_long_range_B_refined	9.976
r_long_range_B_other	9.976
r_scangle_other	8.407
r_dihedral_angle_1_deg	7.669
r_scbond_it	6.326
r_scbond_other	6.326
r_mcangle_it	5.693
r_mcangle_other	5.692
r_mcbond_it	4.24
r_mcbond_other	4.156
r_angle_refined_deg	1.586
r_angle_other_deg	1.194
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	5132
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	132

Software

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