6ZMZ | pdb_00006zmz

UDPG-bound Trehalose transferase from Thermoproteus uzoniensis

X-RAY DIFFRACTION

---

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
2.02	39.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.045	α = 90
b = 69.327	β = 90
c = 98.912	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	1.9	98.9	99.3	0.065	0.077	0.041	0.999	14.6	6.5		29213			39.056

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	1.9	1.94	98.5		1.337	1.58	0.836	0.508	1.3	6.7

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	1.9	56.771	29172	1445	99.036	0.187	0.1847	0.19	0.2227	0.23	39.5

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]
1.214			-1.036		-0.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.086
r_dihedral_angle_4_deg	17.693
r_dihedral_angle_3_deg	13.001
r_lrange_it	6.53
r_lrange_other	6.519
r_dihedral_angle_1_deg	6.501
r_scangle_it	4.97
r_scangle_other	4.969
r_mcangle_it	3.418
r_mcangle_other	3.417
r_scbond_it	3.098
r_scbond_other	3.097
r_mcbond_it	2.35
r_mcbond_other	2.347
r_angle_refined_deg	1.351
r_angle_other_deg	1.267
r_symmetry_xyhbond_nbd_refined	0.247
r_nbd_other	0.212
r_nbd_refined	0.202
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.164
r_nbtor_refined	0.158
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3184
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	43

Software

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