9LHW | pdb_00009lhw

Crystal structure of a wild-type tagose isomerase (TsT4Ease WT) from Thermotogota bacterium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.1 M Tris pH 8.5, 0.2 M Lithium sulfate monohydrate, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.86	α = 90
b = 108.212	β = 108.05
c = 138.775	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2024-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.979183	SSRF	BL10U2

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	2.55	48.95	99.29	0.979	23.2	11.1		94037

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	2.55	2.62			0.492

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	48.95	89434	4525	99.29	0.23049	0.22865	0.2398	0.26695	0.2735	RANDOM

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]
1.12		-2.31	-0.3		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.992
r_long_range_B_other	16.178
r_long_range_B_refined	16.173
r_dihedral_angle_2_deg	13.946
r_mcangle_it	10.296
r_mcangle_other	10.296
r_scangle_other	9.839
r_dihedral_angle_1_deg	7.704
r_mcbond_it	6.665
r_mcbond_other	6.663
r_scbond_it	6.15
r_scbond_other	6.15
r_angle_refined_deg	0.948
r_angle_other_deg	0.352
r_chiral_restr	0.101
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	19720
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
xia2	data reduction
PHASER	phasing