7WRT | pdb_00007wrt

X-ray structure ofThermus thermophilus HB8 transketorase demonstrate in complex with TPP and D-erythrose-4-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	100mM imidazole/MES buffer pH 6.5, 20%(v/v) ethylene glycol, 10% (w/v) PEG 8000, 24mM of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, and N-acetyl-D-glucosamine

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.68	α = 72.308
b = 88.86	β = 88.696
c = 117.37	γ = 73.459

Symmetry
Space Group	P 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 6M		2019-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	41.86	98.1	0.998	18.6	3.5		124659

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31			0.839

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2E6K	2.25	41.86	124659	6251	98.152	0.205	0.202	0.21	0.254	0.25	55.66

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]
-0.409	-0.111	0.005	0.057	-0.084	0.172

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.727
r_dihedral_angle_4_deg	17.546
r_dihedral_angle_3_deg	17.407
r_lrange_it	9.752
r_lrange_other	9.752
r_dihedral_angle_1_deg	7.712
r_mcangle_it	7.239
r_mcangle_other	7.239
r_scangle_it	7.237
r_scangle_other	7.237
r_mcbond_it	5.185
r_mcbond_other	5.185
r_scbond_it	5.013
r_scbond_other	5.013
r_angle_refined_deg	1.642
r_angle_other_deg	1.256
r_nbd_refined	0.212
r_symmetry_nbd_other	0.187
r_symmetry_xyhbond_nbd_refined	0.183
r_metal_ion_refined	0.174
r_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.166
r_nbd_other	0.161
r_symmetry_nbd_refined	0.111
r_symmetry_xyhbond_nbd_other	0.104
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_xyhbond_nbd_other	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20280
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	156

Software

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