6ZJH | pdb_00006zjh

Trehalose transferase from Thermoproteus uzoniensis soaked with trehalose

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	6.5	292	Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.433	α = 90
b = 68.387	β = 90
c = 110.753	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		2019-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976200	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	110.75	99.7	0.074	0.088	0.048	0.999	11.8	6.2		27421

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			1.576	1.889	1.029	0.5		6

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	2.1	58.188	27370	1381	99.535	0.202	0.1997	0.21	0.2445	0.25	52.412

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]
3.211			-3.559		0.347

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.675
r_dihedral_angle_4_deg	17.724
r_dihedral_angle_3_deg	16.889
r_lrange_it	6.896
r_lrange_other	6.885
r_dihedral_angle_1_deg	6.547
r_scangle_it	5.069
r_scangle_other	5.068
r_mcangle_it	4.119
r_mcangle_other	4.119
r_scbond_it	3.111
r_scbond_other	3.11
r_mcbond_it	2.661
r_mcbond_other	2.66
r_angle_refined_deg	1.276
r_angle_other_deg	1.133
r_nbd_refined	0.187
r_symmetry_nbd_refined	0.183
r_symmetry_nbd_other	0.172
r_nbd_other	0.159
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.128
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.055
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3170
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	29

Software

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