6PNT | pdb_00006pnt

Structural Characterization of UDP-glycosyltransferase from Tetranychus Urticae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IYA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	5% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% PEG 5000

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.481	α = 90
b = 77.481	β = 90
c = 130.953	γ = 120

Symmetry
Space Group	P 31 2 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 EIGER X 16M		2019-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	40	99.3	0.083	0.083	0.09	0.032	33.32	8.2		39554

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	99.2		0.627	0.627	0.684	0.267	0.731	1.9	6.2

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 (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	2IYA	1.85	29.88	37336	1944	99.32	0.1701	0.1682	0.1768	0.2079	0.218	RANDOM	31.231

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]
-0.45	-0.22		-0.45		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.553
r_dihedral_angle_4_deg	23.809
r_dihedral_angle_3_deg	13.02
r_dihedral_angle_1_deg	5.93
r_angle_other_deg	2.316
r_angle_refined_deg	2.042
r_chiral_restr	0.142
r_bond_other_d	0.034
r_bond_refined_d	0.017
r_gen_planes_other	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3357
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing