7WRR | pdb_00007wrr

X-ray structure of Thermus thermophilus HB8 transketorase in complex with TPP and MES

X-RAY DIFFRACTION

---

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, N-acetyl-D-glucosamine

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.72	α = 72.564
b = 88.84	β = 88.743
c = 117.61	γ = 73.74

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		2018-05-16	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	2.01	46.67	97.7	0.997	17.6	3.5		175041

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	2.01	2.06			0.732

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	2.01	46.67	175041	8735	97.751	0.199	0.1977	0.2	0.2284	0.23	43.074

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]
0.088	-0.94	2.01	-0.478	-0.47	-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.116
r_dihedral_angle_4_deg	18.411
r_dihedral_angle_3_deg	16.474
r_dihedral_angle_1_deg	7.391
r_lrange_other	7.041
r_lrange_it	7.04
r_scangle_it	5.372
r_scangle_other	5.372
r_mcangle_it	4.651
r_mcangle_other	4.651
r_scbond_it	3.69
r_scbond_other	3.686
r_mcbond_it	3.471
r_mcbond_other	3.471
r_angle_refined_deg	1.611
r_angle_other_deg	1.35
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.191
r_metal_ion_refined	0.191
r_nbd_other	0.184
r_nbtor_refined	0.168
r_xyhbond_nbd_other	0.167
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.132
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	525
Heterogen Atoms	156

Software

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