6ZN1 | pdb_00006zn1

Trehalose transferase bound to alpha-D-glucopyranosyl-beta-galactopyranose from Thermoproteus uzoniensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		apo-Tret

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.6	292	Bis-Tris Propane, PEG 3350, potassium thiocyanide, PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.01	α = 90
b = 68.771	β = 90
c = 110.868	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97630	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	60	99.9	0.054	1	24.36	12.4		47789			34.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	99.94		1.568	0.69	1.47

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	apo-Tret	1.75	58.509	47789	2329	99.985	0.204	0.2021	0.21	0.2345	0.24	39.646

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]
1.109			-1.346		0.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.806
r_dihedral_angle_3_deg	13.953
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_1_deg	6.556
r_lrange_it	5.99
r_lrange_other	5.99
r_scangle_it	4.095
r_scangle_other	4.094
r_mcangle_it	3.628
r_mcangle_other	3.627
r_scbond_it	2.618
r_scbond_other	2.617
r_mcbond_it	2.39
r_mcbond_other	2.384
r_angle_refined_deg	1.309
r_angle_other_deg	1.202
r_nbd_other	0.3
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.198
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.128
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3210
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	56

Software

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